This paper proposes selective deposition of electrospun alginate-based nanofibers through a charged shadow mask to form an array of nonwoven microspots on cell-repelling hydrogel surfaces; subsequently, the target cells are seeded onto these nanofiber-based extracellular matrix (ECM) scaffolds to create cell-based microarrays. The needle tip contains a drop of a blended solution of alginate and polyethylene oxide (PEO); an Al-coated glass shadow mask with micron-sized holes was used for selective deposition to form the patterned microspots of nonwoven mats. The shadow mask was applied with a suitable voltage to repel the nanofibers from its surface, while simultaneously forcing them into the micron-sized holes and onto the cell-repelling hydrogel surface. The electric-field distribution of the electrostatic focusing through the charged shadow masks was numerically simulated and characterized. The experimental results show that when the shadow mask is applied with a higher voltage, a larger dense central spot will be produced within the hole; in addition, the diameter is significantly reduced but the degree of diameter uniformity among the electrospun nanofibers improves. An array of 3x3 nonwoven microspots was successfully demonstrated to selectively deposit alginate-based nanofibers for cell patterning. BHK-21 fibroblast cells were shown to selectively adhere onto the nonwoven microspot surfaces due to the existence of the cell-repelling hydrogel around the microspots. The presented technique is simple and does not require complex surface modifications to selectively seed the target cells onto these micron-sized nanofiber-based ECM scaffolds for potential applications in cell biology and tissue engineering.