Updated

By hijacking planes from U.S. airports on Sept. 11, 2001, and flying them into the Pentagon and the World Trade Center, terrorists killed thousands of innocent people and first responders and revealed an ugly truth: Our airports were not safe.

Today, thanks to a decade of American ingenuity and innovation, many of those security holes have been patched.

Airports are using new technologies, like refined X-ray backscatter equipment, which enables intimate searching of a passenger without the need for them to strip or be stripped by federal agents.

Soon, removing your footwear and coat and throwing away your bottled water, will be a “thing of the past” for air travelers in the U.S., said Peter Kant, executive vice president of Rapiscan Systems, which is working with the Transportation Security Administration (TSA), to improve gate security.

“There’s new machinery in process that will allow screened passengers to keep their shoes on while moving through checkpoints,” Kant told FoxNews.com.

Those baggage handlers may still "touch your junk," but tremendous changes have made air travel safer and securer.

Behind the scenes at LAX's Terminal Five, computing giant Siemens AG installed new baggage screening systems that let passengers drop off their luggage as soon as they get to the airport.

“Delta Airlines found that they went from processing 200 to over 500 bags an hour with this system,” Megan Zaroda, a spokeswoman for Siemens in New York City, told FoxNews.com. “TSA said that it’s removed congestion and minimized safety risks in airport lobbies.”

Yet another technology coming to the nation’s airports: video surveillance equipment that lets the feds detect “abnormal” behavior in crowds, said Michael Silevitch, a professor at Northeastern University in Boston, and co-director of ALERT, a Department of Homeland Security-funded science and technology R&D center.

“This technology was used successfully, after the fact, to identify the Times Square bomber from the rest of the crowd,” Silevitch said.

And new sensors will identify dangerous individuals who have “explosive residue” on their clothing, so would-be bombers don’t even get into an airport, he said.

“These portable sensors could be used outside of the airport itself to identify dangerous individuals or vehicles before they get close enough to do damage,” he added.

Technology gurus aren't promising that TSA will no longer touch your “junk,” as software programmer John Tyner said last fall after an incident with agents at the airport in San Diego. But they do foresee a kind of return to normalcy at the nation’s airports, and even cargo ports, in the coming years.

Funding for so-called “port security” has increased by about 700 percent in the last 10 years, according to an estimate provided to FoxNews.com by the Georgia Center of Innovation for Logistics, a program of the Georgia Department for Economic Development.

Most of this funding comes from the government and agencies like the U.S. Customs and Border Patrol, the U.S. Coast Guard, and the port authorities that own, maintain, and manage the physical infrastructure of airports, bus terminals and seaports.

The federal government spent $259 million on port security efforts in fiscal year 2001; by 2005 the figure had climbed to $1.6 billion per year, and that has increased under the current administration. The money has gone to port authorities in New York, New Jersey, Philadelphia, Baltimore, Miami and New Orleans. And of course, the Department of Homeland Security itself was created after 9/11.

Private sector firms that operate terminals have also invested heavily in IT security during the last 10 years. For cargo screening, for example, new technologies include "non-computed tomography transmission X-rays," explosive trace-detection devices, large-scale gamma ray machines, and even hand-held radiation detection devices, Anne Isenhower, a spokeswoman for the Georgia Center of Innovation for Logistics, told FoxNews.com.

Also behind the scenes, police and border patrol are using IT to share data more quickly than before 9/11. “Before the terrorist attacks, data could only be shared between agencies that were working off the same databases,” said Mike Sullivan, a spokesman for CODY Systems, a government IT provider. “Advancements in technology now allow data to be shared despite the use of disparate databases among agencies, which leads to more intelligence-led policing.”

Sullivan notes that a terror suspect was arrested at the airport, en route to Pakistan, based on the partial VIN number on the car used in the attempted bombing. “Officers were able to identify the original owner of the vehicle which then led them to identify the suspect, all within 48 hours of the incident,” says Sullivan.

And more innovations, pioneered by American IT firms, are in the offing.

“The airport of the future will have security tiers, allowing passengers that submit to advanced background checks and pre-screening more leeway when it comes to security scans,” Kant told FoxNews.com. “Other passengers will have to pass more rigorous, on-premises checks.”