Injection molding of thin-wall parts with microscale surface grooves of polypropylene (PP) and cyclo-olefin copolymer (COC) were performed for this study. Effects of cavity thickness and process conditions on processability, surface replication, and higher-order structure of the molded products were evaluated. Surface replication and optical anisotropy of molded products were analyzed using a polariscope, a polarizing optical microscope, SEM, and a confocal laser scanning microscope. Optical anisotropy in the vicinity of the gate was higher than that at any other position; also, optical anisotropy increased with decreased cavity thickness. The replication property at the center area was more pronounced than those of the flow end and the gate vicinity. The distribution of the replication ratio inside the product decreased with increasing mold temperature. Results showed that the replication properties were correlated closely with skin-shear layer thickness inside the products, and that the replication ratio was lower for greater thickness of the skin-shear layer.