Analytical sample preparation techniques are essential for assessing chemicals in various biological matrices. The development of extraction techniques is a modern trend in the bioanalytical sciences. We fabricated customized filaments using hot-melt extrusion techniques followed by fused filament fabrication-mediated 3D printing technology to rapidly prototype sorbents that extract non-steroidal anti-inflammatory drugs from rat plasma for determining pharmacokinetic profiles. The filament was prototyped as a 3D-printed sorbent for extracting small molecules using Affinisol^TM, polyvinyl alcohol, and triethyl citrate. The optimized extraction procedure and parameters influencing the sorbent extraction were systematically investigated by the validated LC-MS/MS method. Furthermore, a bioanalytical method was successfully implemented after oral administration to determine the pharmacokinetic profiles of indomethacin and acetaminophen in rat plasma. The C_max was found to be 0.33 ± 0.04 µg/mL and 27.27 ± 9.9 µg/mL for indomethacin and acetaminophen, respectively, at the maximum time (T_max) (h) of 0.5–1 h. The mean area under the curve (AUC_0–t) for indomethacin was 0.93 ± 0.17 µg h/mL, and for acetaminophen was 32.33± 10.8 µg h/mL. Owing to their newly customizable size and shape, 3D-printed sorbents have opened new opportunities for extracting small molecules from biological matrices in preclinical studies.