Nanoscale structures have attracted a lot of attention in various fields in recent years. Tip-based nanomanufacturing (TBN) process has proven to be a promising technique for fabrication of nanostructures on single crystal SiC. This study investigates the deformation and removal mechanism of SiC under different scratching directions in TBN process by molecular dynamics (MD) simulations. By analyzing the dislocation glide motion and the phase transformation mechanism of SiC, the deformation type that occurs during TBN process was found to be principally the sliding motion of the primary slip system (recoverable elastic slip motion and dislocation glide motion) and the phase transformation (amorphization and sp3→sp2-like structure transition). This study also shows that the deformation mechanism of SiC during processing is controllable and can be achieved by simply changing the feed direction. The results in this paper can provide direct guidance for the processing of nanogrooves in SiC materials.