Electrospun polyamide 6 (PA 6) and polyamide 6/6 (PA 6/6) nanofibers were produced in order to investigate their experimental characteristics with the goal of obtaining filtration relevant fiber media. The experimental design model of each PA nanofibers contained the following variables: polymer concentration, ratio of solvents, nanofiber media collection time, tip-to-collector distance, and the deposition voltage. The average diameter of the fibers, their morphology, basis weight, thickness, and resulting media solidity were investigated. Effects of each variable on the essential characteristics of PA 6/6 and PA 6 nanofiber media were studied. The comparative analysis of the obtained PA 6/6 and PA 6 nanofiber characteristics revealed that PA 6/6 had higher potential to be used in filtration applications. Based on the experimental results, the graphical representation—response surfaces—for obtaining nanofiber media with the desirable fiber diameter and basis weight characteristics were derived. Based on the modelling results the nanofiber filter media (mats) were fabricated. Filtration results revealed that nanofiber filter media electrospun from PA6/6 8% (w/vol) solutions with the smallest fiber diameters (62–66 nm) had the highest filtration efficiency (PA6/6_30 = 84.9–90.9%) and the highest quality factor (PA6/6_10 = 0.0486–0.0749 Pa−1).