The multilayered, multifaceted and multinational security system that has been constructed to protect the United States from terrorists led to denial of visas to 2.2 million of 9 million foreign applicants last year, according to data presented Wednesday to the Senate Homeland Security and Governmental Affairs Committee.

An additional 2,600 individuals with outstanding visas for the United States were identified by the National Targeting Center run by U.S. Customs and Border Protection (CBP) as having new derogatory information developed about them. That information was passed on to airlines with a recommendation that these high-risk individuals not be permitted to board U.S.-bound aircraft.

The CBP generates nearly 200 targets a day for its center, causing research to determine whether these individuals are indeed high risk.

The Transportation Security Administration’s program, called Secure Flight, begins at the airport when you show your driver’s license or other government ID with your name, birth date and gender. That program vets more than 2 million passengers daily, and within 10 seconds determines whether a boarding pass should be printed.

On average, Secure Flight blocks 25 people a month from boarding planes, according to last week’s hearing, where Homeland Security (DHS) and State Department officials detailed the overlapping computerized programs, agency centers and investigative techniques that have been lashed together to prevent anyone with a threatening background to travel unabated to the United States.

The initial barrier for foreigners is getting a visa, which since 2004 has required fingerprinting as well as photographing of potential travelers, even those from the 36 countries in the visa waiver program.

A new State Department Internet platform, called the Consular Electronic Application Center, is currently available for non-immigrant visas and soon will be able to handle immigrant visas as well. It will permit electronic submission of applications and photos, allowing review before applicants appear for required personal interviews.

The online forms are “smart,” Assistant Secretary of State Janice Jacobs told the panel, which means “irregular” answers are flagged to ensure that officers address them in the interview.”

Each applicant has an electronic scan of the index finger of each hand, and should a person have a cut, blister or skin injury, a visa will not be issued until a fingerprint can be taken.

At the consular office, names are checked against the Consular Lookout and Support System, State’s database of 39 million cases that hold derogatory information about 27 million individuals. Almost 70 percent of that information came from the CIA, Drug Enforcement Administration and Homeland Security, along with an estimated 1 million known or suspected terrorists carried by the FBI’s Terrorist Screening Center.

At the same time the name goes through DHS’s United States Visitor and Immigrant Status Indicator Technology (US-VISIT), which has biographic data based on prior arrival and departure information. It is also connected to the FBI’s criminal master file of some 69 million identities.

US-VISIT also has an automated storage and analytic system known at IDENT, which matches digital fingerprints and photographs with its own watchlist of 6.2 million known or suspected terrorists, as well as criminal and immigration violators.

The Defense Department’s Automated Biometric Identification System contains not just fingerprints of foreign combatants taken on the battlefields but also latent fingerprints retrieved from IED (improvised explosive device) fragments. That system is not yet automated into the US-VISIT program, but it can be searched manually if necessary.

Two Iraqi terrorists who came into the United States under a refu­gee program two years ago — without being discovered — were exposed by an informant in Kentucky and arrested in May 2010. It was only in January of this year that the FBI found that Defense had one of their fingerprints on file, taken from an IED in Iraq.

At the hearing, Sen. Rand Paul (R-Ky.) was told the FBI may have had the prints but not shared them. Paul has since held up Senate approval to extend FBI Director Robert Mueller’s tenure for two more years until he gets answers to several question, including why the Iraqi’s prints were not discovered when they were approved in the refu­gee program.

The State Department since 2009 has been using electronic facial recognition techniques on all visa applications. It now has 142 million images in its database. It is expanding the system with iris recognition technology. This military has used this system extensively in Afghanistan and Iraq, and State hopes soon to use the Defense iris database in its visa screenings.

When foreign travelers arrive in the United States they are photographed and fingerprinted. The images are automatically checked against those supplied with the original visa to make sure they are the same people, a step that reduces passport fraud.

A new DHS system coordinated with State now updates new derogatory information on individuals with approved visas, some of whom may already be in the country. Over the past eight months, the system has seen the revocation of 782 visas.

One weakness that still needs work — the hundreds of thousands who overstay their visas. There is no biometric exit system and until recently there was a backlog of 1.6 million “overstayed” foreign visitors whose status was not known. In April, the Government Accountability Office found that 843,000 of them had either gone or had their status changed.

The remaining 757,000 are being vetted through CBP’s Advanced Targeting System and names are being sent to the National Counterterrorism Center to see if any derogatory information has turned up on them. That process will allow Immigration and Customs Enforcement to prioritize for investigation and removal. DHS Under Secretary Rand Beers told the committee that anyone who overstayed “if they apply for a [new] visa they’ll be denied.”