The edges of van der Waals materials exhibit unique physical and chemical properties, and they are promising for applications in many fields, such as optoelectronics, energy storage, and catalysis. Van der Waals material nanostructures with a controllable high density of edges are difficult to produce by current fabrication methods. In the present study, a simple nanomachining process to fabricate van der Waals nanowires with a high density of edges is proposed. This method used a linear-edge diamond tool to cut the basal plane of van der Waals film materials into a one-dimensional nanowire at the nanoscale. Experimental tests were performed to investigate the influences of the cutting thickness, film thickness, cutting direction, and material properties on the machining outcomes. The results showed that the van der Waals materials possessed low Young's moduli ranging from 24 to 238 GPa by cutting with a cutting thickness of larger than 30 nm, and the out-of-plane cutting direction led to the best machining quality and controllable preparation of van der Waals nanowires. To support the interpretation of the process outcomes, molecular dynamics simulation and transmission electron microscopy were performed to reveal the material-removal mechanism during nanocutting of van der Waals materials. From analysis of the chip-deformation process, interlayer slipping was found to dominate the plastic processing of the van der Waals materials, accompanied by intralayer bending and intralayer fracture in the out-of-plane cutting direction. By contrast, the brittle removal state occurred when cutting in the in-plane direction. This study provides important insights into the material-removal mechanism of van der Waals materials prepared by nanoscale mechanical cutting.