Fe49Pt51 thin films with a thickness of 20 nm were deposited by conventional dc co-sputtering at substrate temperature of 400 and 500°C before undergoing glow-discharge-induced ion bombardment at room temperature. The energy of the incident Ar ions was adjusted by applying a radio-frequency bias (Vb) in the range of 50 to 600 V. Significant abilities of ion bombardment in modifying both chemical ordering and surface morphology are demonstrated. With Vb in the range of 50 to 150 V, the bombardment smoothes the surface and enhances ordering by promoting surface diffusion. Bombarding at high Vb greater than 200 V evolves the surface morphology towards discontinuous island-like structure or rough pinhole topography and causes disordering by progressive etching. The magnetic properties can be tuned with the structural transformations by ion bombardment. The coercivity (Hc) can be increased from 0.57 to 0.75 MA/m by improving ordering for the films deposited at 400°C. On the other hand, the disordering and mass loss may produce the magnetic softening and drastically reduced magnetization.