Abstract The effectiveness of a series of optically transparent aligners for orthodontic treatments depends on the anchoring of each tooth. In contrast with the roots, the crowns’ positions and orientations are measurable with intraoral scans, thus avoiding any X-ray dose. Exemplified by two patients, we demonstrate that three-dimensional crown movements could be determined with micrometer precision by registering weekly intraoral scans. The data show the movement and orientation changes in the individual crowns of the upper and lower jaws as a result of the forces generated by the series of aligners. During the first weeks, the canines and incisors were more affected than the premolars and molars. We detected overall tooth movement of up to about 1 mm during a nine-week active treatment. The data on these orthodontic treatments indicate the extent to which actual tooth movement lags behind the treatment plan, as represented by the aligner shapes. The proposed procedure can not only be used to quantify the clinical outcome of the therapy, but also to improve future planning of orthodontic treatments for each specific patient. This study should be treated with caution because only two cases were investigated, and the approach should be applied to a reasonably large cohort to reach strong conclusions regarding the efficiency and efficacy of this therapeutic approach. Data The repository contains the data of the intraoral scans and all data where manual interactions were performed to allow reproducing the results. The directory and file names are as follows: Name Level, type Description p_Clinical_Trial 1st, directory Patient p: p=3485 stands for patient A, p=6457 stands for patient B Bottmedical 2nd, directory Planning data Sirona 2nd, directory Intraoral scan data Tn 3rd, directory Time step n for n=0: before treatment, n=1-9: after 1-9 weeks of treatment; n=10: end of treatment Lower_Aligner_n_cut1.stl 4th, file Manually cut surface mesh of planned data, lower jaw for time step n Upper_Aligner_n_cut1.stl 4th, file Manually cut surface mesh of planned data, upper jaw for time step n p_OnyxCeph3_Export_j_cut1.stl 4th, file Manually cut surface mesh from intraoral scan, for lower (j=UK) or upper (j=OK) jaw p_OnyxCeph3_Export_j.stl 4th, file Original surface mesh from intraoral scan, for lower (j=UK) or upper (j=OK) jaw teethSeg 4th, directory Segmented crowns via OnyxCeph3 TM teethSeg_noSnap_TolS 4th, directory Transferred crown segmentations and occlusion plane points p_Zi.stl 5th, file Surface mesh of crown segmentation for tooth number i of patient p p_j.stl 5th, file Surface mesh of all crown segmentations for lower (j=UK) or upper (j=OK) jaw of patient p p_j_occPlane.mat 5th, file Binary Matlab file of saved variable occPlane, which defines transferred occlusion plane points for lower (j=UK) or upper (j=OK) jaw of patient p File formats: stl files describe an unstructured triangulates surface by vertices and triangles. These files can be read by the open source software freecad or the MATLAB function stlread. mat files are MATLAB files and can be read via MATLAB function load.