Deep understanding of the effects associated with fabrication parameters and their influence on the resulting structures shape is essential for the further development of direct laser writing (DLW). In particular, it is critical for development of reference materials, where structure parameters are precisely fabricated and should be reproduced with use of DLW technology. In this study we investigated the effect of various fabrication and preparation parameters on the structural precision of interest for reference materials. A well-studied photo-curable system, SZ2080 negative photo-resist with 1 wt.% Michler’s ketone (Bis) photo-initiator, was investigated in this work. The correlation between applied laser power, laser velocity, fabrication direction on the deviations in the structure shape were observed by means of white light interferometry microscopy. Moreover, influence of slicing and hatching distances as well as prebake time were studied as function of sample shape. Deviations in the structure form between the theoretically expected and the one detected after DLW fabrication were observed in the range up to 15%. The observed shape discrepancies show the essential importance of fine-tuning the fabrication parameter for reference structure production.