This study investigates changes in the mechanical and morphological properties (hardness, elastic modulus, surface roughness and dimensions) of a FIB-milled glassy carbon (GC) micro-mold heat treated at 1400 °C for different time periods (0, 10, 20 and 30 min) using nano/micro-indentation, an optical microscope (OM), optical interferometer, scanning electron microscope (SEM) and atomic force microscope (AFM). As the temperature hold-time is increased, the optical appearance of the FIB-milled surfaces is seen to change as a result of both the diffusion of gallium into the surface and the evaporation of the exhaustible gallium source. Additionally, the FIB-milled depth increased by 25–30 nm after heat treatment regardless of increasing the temperature hold-time. The surface roughness for both milled and un-milled surfaces increased to less than Ra = 5 nm with an increase of the temperature hold-time. Both the uniform distributions and the highest values of the hardness and elastic modulus for the GC mold were obtained after heat treatment at 1400 °C for 10–20 min.