I used the CTX 5500 to keep bombs off your plane. I also go elbows deep in your underwear.

The suitcase was ticking.

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It was my third week on the job as one of 55,000 new airport screeners employed by the Transportation Security Administration, and the first day of the war in Iraq. The nationwide terror alert was at orange, and a pair of National Guardsmen patrolled the sprawling departure lobby of the US Airways terminal at LaGuardia, rifles at the ready, gas masks strapped to their thighs. All this made the egg-timer click coming from the bag, a black rolling cart with a pull-up handle, a matter of some urgency.

Michele Asselin

I had picked up the suitcase after it was singled out by one of the cream-colored, SUV-sized machines that x-ray checked luggage. I put it on a metal examination table, as I had been trained to do, and swabbed the surface with a cloth-tipped wand. It tested negative in the explosive trace detector. I unzipped the bag gingerly and faced a jumble of women's clothes, mostly polyester and flowered, then stuck in a latex-gloved hand to feel for solid objects. Almost immediately I discovered an item dense enough to have been flagged as a possible explosive – it was hair cream. But no clock, no bomb, and no explanation for the ticking. The sound stopped when I lifted up the bag, then started again when I set it down.

Behind the frosted-glass partitions near the check-in counter, $5 million worth of bomb detection technology buzzed around me. None of it could help. Once the machine identified out a suitcase as suspicious, it was my job to search it by hand. The only way to determine the source of the ticking came down to a $13.21-an-hour worker: I'd need to follow my trainer's instructions and go EDU – elbows deep in underwear.

So far I had seen the machines flag plenty of deodorant sticks, toothpaste tubes, and shoe heels, which showed up on the screen outlined in red. I had handled sex toys, machetes, and pistols (legal in checked bags). But the closest thing I had seen to a bomb were manufactured images on the screen created by the Threat Image Projection System, a software package developed by the government to make sure we were paying attention. Every once in a while, I learned, police let drug dogs find contraband so they don't grow discouraged. I didn't much care for the implied comparison.

The ticking was real enough, though, and I couldn't let the suitcase through until I'd figured out the origin of the sound. A US Airways supervisor was hovering nearby, and jittery fliers were peeking at us through the breaks in the partitions. I took everything out, stacking clothes on the table. I felt around the lining. I turned the suitcase over once more, noted that the ticking stopped, and saw a bulge in a tiny pocket tucked between the rods for the extendable handle. It was an electric toothbrush that turned on when it pressed against the table but was packed too tight to vibrate.

Picking through other people's skivvies was my very small part in a very big government initiative. "You're looking for a needle in a haystack," says Larry Johnson, a former deputy director in the State Department's Office of Counterterrorism in the early 1990s. Except you're doing it through a barn wall, without knowing which day the needle will arrive or what it might look like when it does. More than 4 million checked bags pass through the nation's 429 commercial airports on any given day, and since the beginning of the year, the Transportation Security Administration has been charged with examining all of them, on the slim chance that one contains a bomb. The ultimate ideal would mean trained workers going through every piece of luggage by hand. Since that's obviously impractical, the TSA depends on technology – the same basic technology that screens passengers and carry-on bags.

The first stop for checked bags is what's called a CTX machine, which uses conventional X-ray technology as well as a CT scanner that slices beams through a piece of luggage to determine the density and volume of the contents. (The machines are made by two certified manufacturers, but the CTX 5500, built by InVision, predominates to such an extent that the brand name has become shorthand for the device.) "If you run a bomb through it, it will find it nearly 100 percent of the time," says Doug Laird, a former security chief of Northwest Airlines.

The problem is that the CTX flags a whole lot of other things with the same volume and density as some explosives. These include peanut butter, toothpaste, chocolate, golf balls, shoe heels, Blow Pops, and, believe it or not, live crabs. The device also alerts screeners to any item it can't see through: laptop computers, camera equipment, cell phones, oxygen tanks, golf club heads, and physics textbooks.

How flawed is the CTX? It stops 18 to 35 percent of all bags, depending on who's giving the numbers. False positives waste a lot of money; the machines cost millions, and more hand-searches mean more wage-earning workers, raising the total cost of airport security to $5 to $7 per passenger. More important, false positives undermine the efficacy of hand searches. A few alarms a day and screeners investigate every one thoroughly. A few dozen and they become inured to the routine.

The current system discourages screeners from thinking for themselves, says Issac Yeffet, a former security chief of El Al who's now a consultant based in Manhattan. "Let's say I'm a screener, and I open the luggage to do a search and find chocolate or peanut butter – I'm happy because I found what the machine flagged." Although the CTX highlights suspect items, screeners don't run bags back through the machine after the hand search to make sure they've correctly identified what really caused the alarm. No one's taught to think in terms of how a would-be terrorist might try to game the system. "I can assure you, from my experience and knowledge," says Yeffet, "that most of the explosives will be in a false bottom."

Yeffet's point is that screeners should be trained not as machine operators but as security personnel. If he's right, the TSA has a long way to go. Even the basic training we received was slapdash. Congress mandates that screeners spend 40 hours in the classroom, but my class spent about half that time. (We got paid for the entire 40.) For four days, we met in a hotel on the perimeter of the airport, where the instructor taught us the rudiments of what constitutes a bomb. He spent the rest of the time asking us about our experiences as New Yorkers since September 11. I touched the machines only once, on a field trip to the airport where we walked into a filthy side room in an airline terminal to find a screener slumped over asleep at a CTX unit. There was a Starbucks cup on top of one of the other devices and a pizza box on a third. I worked a regular shift for five weeks without getting any of my mandated 60 hours of on-the-job training.

The system would be better if more screeners were like one of the guys on my shift, a former military man with a buzz cut and a crease in his pants that could slice bread. A few days after I started, he asked some of us why we were there. An older man who had been in book publishing said that he had to come out of retirement because his 401(k) tanked. One of the younger guys had been a prison guard and thought this would be less demanding; another was finishing a computer science degree and needed a part-time job in his Queens neighborhood. The military man listened to the rest of us and declared, "I wanted to serve my country." When he opened a bag, he purposefully examined each item. He turned tubes of toothpaste over in his hand, shook golf balls, and unfolded clothes.

Most of my colleagues weren't so careful. One screener, a holdover from the private company that ran LaGuardia security before the TSA took over, would sometimes take bags that were supposed to be searched by hand and just leave them on the examination table until another worker, who assumed they had already been cleared, sent them to the plane. One day I was at the controls of the CTX, which ejects bags like a toaster, bouncing them against a hard backstop. Safety regulations required moving the luggage before making even a cursory check. My fellow screener, however, started searching a suitcase where it landed and was hit square in the head by the next bag. That was our interim supervisor.

Some at the Transportation Security Administration are dissatisfied with the CTX. Because the machine is expensive, slow, and has a fairly high rate of false positives, Lyle Malotky, a top scientific and technical adviser at the TSA, acknowledges that the agency is looking for a better system.

Devices that might be deployed are first brought for testing to the TSA's labs, a cluster of connected buildings at the Atlantic City airport. Behind the agency's hangar, there's a storage bunker full of explosives. The parking lot is littered with the dented shells of cargo containers technicians have blown up.

The government funded the CTX machines in the early '90s but, due to the expense, didn't install many in airports. Two months after September 11, Congress ordered nearly 1,000 units as a stop-gap measure. Now Malotky would like to find a more sensitive machine that would support the CTX and make the screening process more efficient. Bags would still go through the CTX first, but anything flagged as suspicious would then be routed to a more sensitive machine that would further winnow down the amount of luggage that needs to be checked by human hands. The idea is that TSA employees could concentrate on searching a smaller number of bags more accurately.

The only way to see what's in a bag or on a person is to bombard the subject with energy – like X rays, neutrons, or radio waves – measure the reaction, and use it to display an image on a screen. The conventional X ray, which came into widespread use during World War I and has been a part of airport security since the '70s, creates a simple two-dimensional image. The CT scan, a computerized cross-sectional X ray, can map a 3-D image in color. As of now, none of the technologies being used can detect every type of substance, so a machine that can spot explosive chemicals might not find metals or radiological materials.

One of the highlights of my tour of the TSA labs is a backscatter X-ray machine, which produces a high-contrast image by bouncing beams against an object and measuring how many return. It can be used to screen luggage, but this model is configured for people. When lab codirector Susan Hallowell asks for volunteers to test the unit, she also offers a warning: "It not only makes you look naked, but fat, too." Grimacing, she steps up to demonstrate. As Hallowell stands against the unit, her body appears as a doughy white blob on the monitor, free of clothes. Also visible are the gun stashed in her belt and a plastic baggie of explosives tucked into her pocket.

It's a remarkable piece of machinery, but there are reasons it's in the lab and not the airport: It's big, slow, and basically shows what someone looks like unclothed. (Thankfully, it leaves fine anatomical details to the imagination.) Already there's a locker-room atmosphere among the screeners, mostly male and bored. Have them stare at practically nude people all day and you're asking for trouble. Still, TSA chief technology officer Randal Null is enthusiastic about backscatter. "We may not put it in every lane," he says. "But we'll use this technology once we deal with the privacy, cost, and size issues."

Another promising technology is X-ray diffraction, which InVision, the company that makes the CTX machines, invested in last year by buying a German firm that makes a diffraction unit called the Yxlon 3000. The device can check only 60 bags an hour – the CTX 5500 can handle about six times that – but it could help reduce false positives. "We believe that the magic bullet is the combination of CT and diffraction," says InVision CEO Sergio Magistri. By having a diffraction machine check what the CTX flags, "you can do 500 bags an hour."

In case diffraction doesn't become the new standard, InVision also owns Quantum Magnetics, a San Diego company that's applying MRI techniques to security by using a process called nuclear quadrupole resonance. It involves shooting low-frequency radio waves into an object to stimulate the nuclei of the atoms in it. The electrical response of each substance is unique, so in theory, the units would pinpoint an explosive without false alarms.

In Atlantic City, the tour is ending and Null takes me to the bag room. Here, the TSA tests new technologies on actual luggage – about 10,000 bags collected from airline lost-and-founds around the country. "If you lost a bag in the past 10 years it probably ended up here," he jokes. When the scientists look at a new system, Null explains, they build a bomb and place it in a piece of luggage selected at random. Then they run that bag and a bunch of others through the unit they're testing to see if it finds the bomb.

What constitutes success? Null's looking for a machine that identifies every bomb while keeping false positives to a tolerable level. That's a formula sure to please passengers – not to mention my former colleagues on the front lines.

• magazine-11.09