The development of transcatheter mitral valve replacement therapies requires accurate post-processing analysis tools to provide D-shaped mitral annulus dimensions from 3-dimensional (3D) data. The agreement between two semi-automated, software packages to process 3D transesophageal echocardiography (TEE) data for the measurement of the mitral valve annulus dimensions was evaluated. 3DTEE data of patients with moderate–severe mitral regurgitation (MR) were postprocessed with semi-automated, vendor-independent (VI) software and vendor-specific (VS) software. Both post-processing software provided key measurements for the selection of transcatheter valve prosthesis size: annulus area, annulus circumference and the septal-to-lateral distance of the annulus. The intertrigonal distance was provided only by the VS software. The inter- and intra-observer agreements were assessed with Bland–Altman analysis. Of 105 patients (63.8 ± 11 years, 66% male) with MR, 28 had secondary MR, 45 fibroelastic deficiency, and 32 Barlow’s disease. Using VS software, the dimensions for the overall population were 16.1 ± 4.6 cm² for annulus area, for circumference 14.4 ± 1.9 cm, intertrigonal distance 3.4 ± 0.5 cm and septal-to-lateral distance 3.8 ± 0.6 cm. Similar dimensions were obtained using VI software: 15.7 ± 4.6 cm² for annulus area, 14.5 ± 2.0 cm for circumference, and 4.1 ± 0.6 cm for septal-to-lateral distance. The inter- and intra-observer agreement for both software programs was excellent. In conclusion, current post-processing software programs for 3DTEE data of the mitral valve annulus provide good reproducibility of key measurements to select the transcatheter prosthesis size.