This study was aimed to compare the consistency between the custom abutment design and the output in two CAD software programs. Materials and Methods: Customized abutments were designed by using 3Shape Dental System CAD software and Delta9 CAD software on a plaster model with implants (CRM STL file). After milling of the designed abutments, the abutments were scanned with a contact method scanner (Test STL file). We overlaid the Test STL file with each CRM STL file by using inspection software, and then compared the milling reproducibility by measuring the output error of the specimens from each CAD software program. Results: The Delta9 showed better milling reproducibility than 3Shape when comparing the milling errors obtained with a full scan of all specimens (P < .05) and also when comparing the axial wall region specifically according to the axial angle. With 0.9 mm marginal radius, the Delta9 showed better consistency between the design and the output than 3Shape (P < .05). While, antirotation form had no significant difference in error between the two systems. When cumulative errors were compared, the Delta9 showed better milling reproducibility in almost cases (P < .05). Conclusion: Delta9 showed a significantly smaller error for most of the abutment design options. This means that it is possible to facilitate generation of printouts with reliable reproducibility and high precision with respect to the planned design.