Researchers often use skulls prepared by different techniques in geometric morphometrics (GM). The main goal of this paper was to compare and measure errors in GM analyses using snake skulls prepared with two of these techniques (microCT Scan and chemical maceration). We evaluate if analyses employing skulls with both types of preparation may generate biased results or if this parameter is negligible. Thirty‐four heads of Liophis miliaris merremi were first scanned and subsequently prepared following the techniques of chemical maceration. We used 37 and 18 landmarks for dorsal and ventral views of skulls respectively. To evaluate shape differences between the same skull assessed by microCT Scan and chemical maceration, we performed discriminant analyses, Hotelling's T2 and cross‐validation tests. Discriminant analyses showed significant differences between preparation techniques for both views. However, all the differences between dried and microCT scanned skulls were smaller than those between individuals of the same taxon, which means that such differences are within the range of intraspecific variation. The results support the use of specimens prepared according to both techniques in studies of GM.