This experimental study investigated the machinability of polymethylmethacrylate (PMMA)/multi-walled carbon nanotube (MWCNT) nanocomposites with 20 wt% MWCNTs in focused ion beam (FIB) micromachining. PMMA/MWCNT nanocomposites were fabricated using a solution casting method, in which PMMA and MWCNTs were dispersed in a solvent by ultrasonication. Microscale rectangular pockets were created on the PMMA/MWCNT nanocomposites to study the material removal mechanism in FIB. Effects of FIB input current and the ion beam overlap parameter (overlap %) on the material removal rate and geometric accuracy were studied. It was observed that the material removal rate increased with increasing input current and decreasing overlap %. Soft lithography was used to translate the ion-milled pockets on PMMA/MWCNT nanocomposites into microscale posts on polydimethylsiloxane (PDMS) for accurate measurement of the pocket geometries. A Scanning Electron Microscope (SEM) was used to investigate the characteristics of the micromachined features, nanocomposite surfaces, and replicated PDMS patterns. Our results demonstrated an effective method to produce microscale patterns on MWCNTbased nanocomposites.