A major challenge in muscle tissue engineering is mimicking the ordered nanostructure of native collagen fibrils in muscles. Electrospun nanofiber constructs have been proposed as promising candidate alternatives to natural extracellular matrix. Here, we introduce a novel method to fabricate a two-dimension (2D) sheet-type and three-dimensionally integrated nanofibrous scaffolds by combining electrospinning and rapid prototyping. The aligned 2D nanofiber mats can be processed into different configurations by the CAD/CAM-based deposition of thermally extruded microstructures. We demonstrate the feasibility of these microstructures for application in muscle tissue engineering by culturing C2C12 myoblasts and then evaluating their viability and alignment. Highly aligned cellular morphologies were successfully achieved along the direction of the nanofibers in all types of scaffolds. The hybrid scaffolds provided mechanical support and served as a topographical guide at the nanoscale, exhibiting their potential to meet the requirements for practical use in tissue engineering applications.