Polymeric microstructures and microchannels are widely used in biomedical devices, optics, microfluidics and fiber optics. The quality, the shape, the spacing and the curvature of microstructure gratings are influenced by different mechanisms and fabrication techniques used. This paper demonstrates a cost-effective way for patterning high-aspect-ratio thermoplastic microstructures using thermal imprint technology and finite element modeling. Polymeric materials polypropylene (PP), polyethylene terephthalate glycol (PETG), polyvinyl chloride (PVC) and styrene-acrylonitrile (SAN) were chosen for the experimental investigations. A finite element model was constructed to define the most suitable parameters (time, heating temperature, pressure, etc.) for the formation of microstructures using the thermal imprint procedure. To confirm the relevance of the finite element model, different types of PP, PETG, PVC and SAN microstructures were fabricated using theoretically defined parameters. Experimental investigations of imprinted microstructures’ morphological and optical properties were performed using scanning electron microscopy, atomic force microscopy and a diffractometer. Obtained results confirmed the relevance of the created finite element model which was applied in the formation of high-aspect-ratio microstructures. Application of this model in thermal imprint would not only reduce the fabrication time, but also would highly increase the surface quality and optical properties of the formed structures.