A femtosecond pulsed Ti:sapphire laser with a pulse width of 120 fs, a wavelength of 800 nm and a repetition rate of 1 kHz was employed for direct write patterning of single crystalline 3C–SiC thin films deposited on Si substrates. The ablation mechanism of SiC was investigated as a function of pulse energy. At high pulse energies (>1 µJ), ablation occurred via thermally dominated processes such as melting, boiling and vaporizing of single crystalline SiC. At low pulse energies, the ablation mechanism involved a defect-activation process that included the accumulation of defects, formation of nano-particles and vaporization of crystal boundaries, which contributed to well-defined and debris-free patterns in 3C–SiC thin films. The interactions between femtosecond laser pulses and the intrinsic lattice defects in epitaxially grown 3C–SiC films led to the generation of nano-particles. Micromechanical structures such as micromotor rotors and lateral resonators were patterned into 3C–SiC films using the defect-activation ablation mechanism.