Geometric Morphometrics (GMMs) is a useful tool for the experimental characterization of different taphonomic modifications on bone surfaces, including anthropogenic cut marks. Until now, most research has been conducted evaluating experimental and non-altered cut marks, in order to obtain a better control of the studied variables. However, in archaeological contexts, bones are frequently subject to different taphonomic alterations and, in most cases, bone surfaces and the associated taphonomic signals show different grades of alteration. In this study, we present an experimental approach in which experimental cut marks were produced, mechanically altered, digitized, and analyzed using GMMs, in order to provide an in-depth characterization of how overlying taphonomic traces can alter cut marks. In the experiment, 40 cut marks were subjected to abrasion by a mixture of distilled water, sands, and gravels, using a tumbling machine in a series of cumulative cycles for a total of 4 h: cycle 1 (0.5′), cycle 2 (0.5′), cycle 3 (1 h) and cycle 4 (2 h). Cut mark cross-section profiles were then obtained using 3D digital microscopy, and a 2D 7-landmark designed for cut mark analyses were employed. Our results show a clear statistical differentiation among non-altered cut marks belonging to Cycle 0, and altered cut marks. The depth and opening angle of cut marks appear to be the features with a higher weight in the differentiation between altered and non-altered cut marks. On the other hand, there are no distinctions when differentiating between the diverse altered cycles. These results, like those previously obtained in an experimental approach using a binocular microscope, point to the limitation of the identification of cut marks and other taphonomic signals in archaeological contexts with altered bone surfaces, caused by the fast alteration and the loss of diagnostic criteria of the bone surface modifications.