Since gas flows in micro/nano devices are dominated by the interaction of gas molecules and solid surfaces, surface modification technique is one of the critical issues for optimizing the thermal performance of these devices. In this paper, we demonstrate the successful application of vertically aligned single-walled carbon nanotubes (VA-SWNTs) as surface modification material to enhance the energy accommodation of gas molecules on surfaces. The scattering of gas molecules on quartz surfaces covered with VA-SWNTs is investigated by the molecular beam technique. The energy accommodation coefficients of helium, which tend to be small even for rough surfaces because of the large mass mismatch between helium and surface atoms, are close to unity on the modified surfaces. The measurement with the free-standing films further reveals that the high accommodation is attributed to the unique morphology of the films with high porosity, which allows gas molecules to penetrate into the films and realizes a large number of collisions with SWNTs. The result suggests that the surface modification with VA-SWNTs can be utilized for the thermal management in electric devices and micro/nano-electro-mechanical systems.