Advanced polymeric materials, such as polyether ether ketones (PEEK), have been placed as direct substitutes for metals and ceramics in diverse applications, such as the machinery industry and biomedical engineering. Moreover, surface treatments allow the emergence of brand-new properties or the improvement of preexisting ones, such as friction, lubrication, wettability, cellular infiltration, or osseointegration. A paramount approach to achieving topographical modifications is by using laser micro/nanoprocessing techniques such as direct laser interference patterning (DLIP). Herein, PEEK foils are structured with DLIP method using ultrashort pulses. The influence of the pulse duration between 266 fs and 15 ps and the pulse-to-pulse overlap on the resulting surface topography and chemistry is assessed. As a result, well-defined line-like textures with a period of 5.8 μm and aspect ratios up to 0.88 are achieved. Furthermore, it is possible to explore and understand the behavior of surface phenomena such as swelling, increase/decrease of laser–material interaction onset, and laser-induced periodic surface structures formation. A comprehensive topographical and chemical characterization study demonstrates that these distinctive topographical features occur because of multiphoton absorption, incubation effects, and heat accumulation. These phenomena allow structuring polymeric substrates that are low-absorbing and challenging to pattern with conventional nanosecond infrared (IR) laser sources.