Being able to obtain a 3D visualization of an object gives significant advantages. Due to it, the internal structure of any sample subjected to a test can be studied. That is the reason for the utilization of micro-tomography in both research and industry. Due to various materials and their properties, there is a difficulty in setting the optimal acquisition parameters. This paper provides the analysis results of different micro-CT scan parameters, for paraffin fixed biological samples. The tested parameters include: averaging on detector, scanning angular range, and sample orientation. The biological samples fixed in the paraffin wax were used for scanning, and then the acquired scans were analysed. The final quality assessment results were obtained by using both quantitative and qualitative methods. The general aim of this work is to find the optimal scan parameters setting, out of the trialled options.