This paper presents an algorithm developed to solve a duplicity problem found during the development of a software system for BIM generation. The chosen schema for the BIM is gbXML. The Manhattan World Assumption is adopted because the objective of the system is to obtain simplified and regularized 3D models of the indoor environment to perform a thermal analysis. At the moment of writing the gbXML, some duplicity and errors were found in the polygons of both sides of walls that divide adjacent rooms. The algorithm presented in this paper was developed to detect and solve these errors. Also, this paper includes the testing and validation of the algorithm. The test is based on the application of the algorithm to six different scenarios of study: four of them are artificial scenarios developed to test the different issues detected and two of them are real cases.