The aim of this study was to construct a novel, repeatable, reproducible, and accurate measurement protocol for the area and volume of the remaining cement after removal of fixed multibracket appliances, the area and volume of remaining cement after cement removal, the area and volume of enamel removed after cement removal, and the volume of cement used to adhere fixed multibracket appliances. A total of 30 brackets were cemented and removed with over 30 extracted teeth embedded into three experimental models of epoxy resin. The models were scanned before and after bracket placement, bracket debonding, and polishing the remaining cement. The brackets were submitted to micro-computed tomography. The standard tessellation language digital files were aligned, segmented, and re-aligned using geomorphometric software. The digital measurement technique accuracy, repeatability, and reproducibility were analyzed using Gage R&R statistical analysis. The variability attributable to the area and volume measurement techniques of the total variability of the samples was 0.70% and 0.11% for repeatability, respectively, and 0.79% and 0.01% for reproducibility, respectively. The re-alignment procedure is a repeatable, reproducible, and accurate technique that can be used to measure the area and volume of the remaining cement after removal of fixed multibracket appliances, the area and volume of remaining cement after cement removal, the area and volume of enamel removed after cement removal, and the volume of cement used to adhere the fixed multibracket appliance.