New additive manufacturing techniques, such as melting electro-writing (MEW) or near-field electrospinning (NFES), are now used to include microfibers inside 3D printed scaffolds as FDM printers present a limited resolution in the XY axis, not making it easy to go under 100 µm without dealing with nozzle troubles. This work studies the possibility of creating reproducible microscopic internal fibers inside scaffolds printed by standard 3D printing. For this purpose, novel algorithms generating deposition routines (G-code) based on primitive geometrical figures were created by python scripts, modifying basic deposition conditions such as temperature, speed, or material flow. To evaluate the influence of these printing conditions on the creation of internal patterns at the microscopic level, an optical analysis of the printed scaffolds was carried out using a digital microscope and subsequent image analysis with ImageJ software. To conclude, the formation of heterogeneously shaped microfilaments (48 ± 12 µm, mean ± S.D.) was achieved in a standard FDM 3D Printer with the strategies developed in this work, and it was found that the optimum conditions for obtaining such microfibers were high speeds and a reduced extrusion multiplier.