4H-SiC (silicon carbide), known as the third-generation semiconductor, has been widely used in high-power electronic devices. However, surface defects on wafers can seriously affect the key parameters and stability of silicon carbide devices. In this work, we pioneered a dual-laser comparative framework to systematically investigate the effects of continuous wave (CW) and femtosecond (FS) pulse laser micromachining on 4H-SiC epitaxial layers. CW laser restructuring optimized lattice integrity at sub-melting thresholds, while ultrafast FS pulse laser achieved submicron roughness control (from 8 μm to <0.5 μm) without obvious thermal collateral damage. To reveal the dynamic mechanism during the laser modification, multi-physics finite element models were adopted that decouple thermal and non-thermal mechanisms. This work expands the feasibility of laser micromachining for next-generation SiC device manufacturing.