In the medical field the additive manufacturing process by fused deposition modeling has gained a great importance given the ability to create complex, organic geometries, in a short time period and the possibility of high customization. By fused deposition process the part is created layer by layer and the resulting part is characterized by high anisotropy, dictated mostly by printing parameters. To alleviate the anisotropy and to study the mechanical behavior of the 3D printed parts thermal processing is used. The materials used as filament is a poly (lactic acid) with copper particles embedded for antibacterial purposes. Samples were 3D printed using a commercial printer, thermally processed and tested in compression. On the failed specimens fracture investigations were performed to understand mechanical behavior during compression. The mechanical characteristics showed improvement and the anisotropy decreased as the processing temperature increased, but the samples became brittle. The mechanical behavior changed drastically on the thermally processed samples because of structural changes: a discontinuity between exterior layers and infill layers was created post layer fusion, the first region being the one stressed and failed first during tests.