This study examined the femtosecond laser ablation properties of core and shell polymers their relationship to the ablation characteristics of core-shell nanofibers. The single-pulse ablation threshold of bulk polycaprolactone (PCL) was measured to be 2.12 J/cm(2) and that of bulk polydimethylsiloxane (PDMS) was 4.07 J/cm(2). The incubation coefficients were measured to be 0.82 +/- 0.02 for PCL and 0.53 +/- 0.03 for PDMS. PDMS-PCL core shell and pure PCL nanofibers were fabricated by electrospinning. The energy/volume of pure PCL and PDMS-PCL core-shell nanofiber ablation was investigated by measuring linear ablation grooves made at different scanning speeds. At large scanning speed, higher energy/volume was required for machining PDMS-PCL nanofiber than for PCL nanofiber. However, at small scanning speed, comparable energy/volume was measured for PDMS-PCL and PCL nanofiber ablation. Additionally, in linear scanned ablation of PDMS-PCL fibers at small laser pulse energy and large scanning speed, there were partially ablated fibers where the shell was ablated but the core remained. This was attributed to the lower ablation threshold of the shell material. (C) 2016 Elsevier B.V. All rights reserved.