We developed two types of high performance nanofiber filters by increasing the uniformity of the fiber layer’s deposition on the substrate media and by fabricating nanofiber with a branched morphology, in which additional fibers were spun to radiate from the main fibers. We subsequently compared them with conventional and beaded nanofiber filters in terms of particle removal efficiency, filter pressure drop, and particle loading capacity. First, the uniformity of the nanofiber’s deposition, which was visually evaluated using optical and electron microscopes, was increased by removing the substrate surface charge during electrospinning. The uniform nanofiber filters demonstrated a higher filtration efficiency with a lower pressure drop than their conventionally electrospun counterparts, which exhibited irregular fiber layers. Second, branched nanofiber was fabricated by adjusting the viscosity of the polymer solution. The performance of the nanofiber filters was dramatically improved by the decrease in air flow resistance, which resulted from (1) a longer distance streamwise between the fibers and (2) a smaller diameter for the fibers. The enhanced efficiency was also due to (3) the additional fibers branching out from the main fibers.