In 2003, he was interviewed for the school's newspaper The Viking Voice about Allen's history with NASA and the future of the agency in regard to the then-recent Space Shuttle Columbia disaster.

Following graduation from flight school, he flew F-4 Phantoms from 1980 to 1983 with squadron VMFA-312 at Marine Corps Air Station Beaufort, South Carolina, and was assigned as Aircraft Maintenance Officer.

His technical assignments have included: Astronaut Office representative for all Space Shuttle issues related to landing sites, landing and deceleration hardware, including improvements to nosewheel steering, brakes and tires, and drag chute design; Shuttle Avionics Integration Laboratory (SAIL), which oversees, checks, and verifies all Shuttle flight control software and avionics programs; Technical Assistant to the Flight Crew Operations Director who is responsible for and manages all flight crew operations and support; lead of the Astronaut Support Personnel team which oversee Shuttle test, checkout, and preparation at the Kennedy Space Center; Special Assistant to the Director of the Johnson Space Center in Houston, Texas; lead of a Functional Workforce Review at the Kennedy Space Center, Florida, to determine minimal workforce and management structure requirements which allow maximum budget reductions while safely continuing Shuttle Flight Operations; Director of Space Station Requirements at NASA Headquarters, responsible for the International Space Station requirements, policies, external communications and liaison with Congress, international partners, and industry.

STS-46 was an 8-day mission aboard the Space Shuttle Atlantis which featured the deployment of the European Retrievable Carrier (EURECA), an ESA-sponsored free-flying science platform, and demonstrated the Tethered Satellite System (TSS), a joint project between NASA and the Italian Space Agency.

The crew also worked around the clock performing combustion experiments and research related to USMP-3 microgravity investigations used to improve production of medicines, metal alloys, and semiconductors.

[11] Allen retired from the Marine Corps and left NASA in October 1997, and is now CEO of Aerodyne Industries in Cape Canaveral, Florida.

[14] In 2017, Allen was recognized by the National Space Club's Florida Committee with the Dr. Kurt Debus Award.

[16] In the spring of 2023, Allen was featured in Space Coast Living magazine,[17] while Embraer included an interview with him in their trade journal, Advantage.