Laser micro-machining of amorphous PEEK has been demonstrated with 180 fs/1 kHz NIR (775 nm) and NUV (387 nm) laser pulses. The single pulse ablation threshold was found to be 2.01 ± 0.05 J/cm2 and 0.23 ± 0.02 J/cm2 at 775 nm and 387 nm respectively. The significant difference in ablation threshold is due to the requirement for 3-photon absorption at 775 nm, where PEEK is transparent while significant linear absorption within the material bandgap occurs at 387 nm, enhancing 2-photon absorption. A high 2-photon absorption coefficient, measured to be β387 ~ 38 cm GW-1 supports this view while at the bandgap edge, 400 nm, β400 ~ 0.7 cm GW-1. Multi-pulse exposure yields incubation coefficients of S775 = 0.72 ± 0.01 and S387 = 0.85 ± 0.02 hence incubation is significantly reduced in the NUV. Ablation of PEEK with NUV fs pulses demonstrates much reduced melting and re-deposition, thus precision NUV polymer micromachining is accomplished while laser induced periodic surface structures (LIPSS) with pitch Λ < 0.4 μm are observed at the base of ablated regions. Scanned areas exhibit white light diffraction due to this sub-micron periodic surface modulation. With the aid of a phase only spatial light modulator, multi-beam NUV micro-structuring is achieved, speeding micro-processing while reaching a line width < 4 μm with NA = 0.4 objective.