To measure the impact of the superimposition method on accuracy analyses in digital implant research using an ISO-recommended 3-dimensional (3D) metrology-grade inspection software (Geomagic Control X; 3D Systems; Rock Hill, South Carolina; USA). A six-implant edentulous maxillary model was scanned using a desktop scanner (7Series; DentalWings; Montreal, Canada) and an intraoral scanner (TRIOS 4; 3Shape; Copenhagen, Denmark) to generate a reference and an experimental mesh. Thirty experimental STL files were superimposed onto the reference model's STL using the core features of six superimposition methods: initial automated pre-alignment (GI group), landmark-based alignment (G1 group), partial area-based alignment (G2 group), entire area-based alignment (G3 group), and double alignment combining landmark-based alignment with entire model area-based alignment (G4 group) or the scan bodies' surface (G5 group). The groups underwent various alignment variations, resulting in sixteen subgroups (n=30). The alignment accuracy between experimental and reference meshes was quantified by using the root mean square (RMS) error as trueness and its fluctuation as precision. The Kruskal-Wallis test with a subsequent adjusted post-hoc Dunn's pairwise comparison test was used to analyze the data (α = .05). The reliability of the measurements was assessed using the intraclass correlation coefficient (ICC). Four hundred and eighty superimpositions were used. No significant differences were found in trueness and precision among the groups (p>.05), except for partial area-based alignment (p<.001). Subgroup analysis showed significant differences for partial area-based alignment considering only one scan body (p<.001). Initial automated alignment was as accurate as landmark-based, partial, or entire area-based alignments (p>.05). Double alignments did not improve alignment accuracy (p>.05). The entire area-based alignment of the scan bodies' surface had the least effect on accuracy analyses. Digital oral implant investigation remains unaffected by the superimposition method when ISO-recommended 3D metrology-grade inspection software is used. At least two scan bodies are needed when considering partial area-based alignments. The superimposition method choice within the tested ISO-recommended 3D inspection software did not impact accuracy analyses in digital implant investigation.