Fused filament fabrication (FFF) represents a straightforward additive manufacturing technique applied in the medical sector for personalized patient treatment. However, frequently processed biopolymers lack sufficient thermal stability to be used as auxiliary devices such as surgical guides. The aim of this study was to evaluate the dimensional accuracy of experimental biocopolyester blends with improved thermal characteristics after printing, annealing and sterilization. A total of 160 square specimens and 40 surgical guides for oral implant placement were printed. One subgroup of each material (n = 10) underwent thermal annealing before both subgroups were subjected to steam sterilization (134 °C; 5 min). Specimens were digitized and the deviation from the original file was calculated. The thermal behavior was analyzed using differential scanning calorimetry and thermogravimetric analysis. A one-way ANOVA and t-tests were applied for statistical analyses (p < 0.05). All biocopolyester blends showed warpage during steam sterilization. However, the material modification with mineral fillers (21–32 wt%) and nucleating agents in combination with thermal annealing showed a significantly reduced warpage of printed square specimens. Geometry of the printing object seemed to affect dimensional accuracy, as printed surgical guides showed less distortion between the groups. In summary, biocopolyesters did benefit from fillers and annealing to improve their dimensional stability.