The replication of polymeric microstructures on a flat surface is not easily achieved by conventional injection molding, because of the required micro-dimensional control and the stringent tolerances of most applications. Moreover, the flow behaviour of melts in micro cavities remains not well understood and challenging. On the other hand, injection-compression molding is all established process for the manufacturing of optical storage media, like compact discs (CD) or digital versatile discs (DVD), with grooves and pits at the micro-scale. The difficulties arise mainly turn two sources: lack of adequate filling because of premature freezing of features with very small thicknesses and excessive deformation during ejection due to high friction at the polymer-metal interface. In this work, a study is carried out to investigate the effect of process parameters on the replication of various microstructures on a flat disk using microinjection-compression molding. A commercial microinjection molding machine has been used in the study. Two optical grade polymers poly(methyl methacrylate) (PMMA) and cyclic olefin polymer (COP) were used in conjunction with various mold inserts to reproduce the embedded microstructures. The dimensions of the microstructures on the inserts card molded parts were measured with a confocal profiler. A transcription ratio was defined to assess the quality of the replication. The design of experiment (DOE) method was used to obtain correlations between the process parameters and the development of the microstructure during injection-compression molding.