Production of prefabricated pipe spools for the needs of the oil and gas industry requires precise determination of their shape and dimensions. The crucial moment of production is to measure the spool being built, compare it with the design and define the geometry corrections that should be applied at the construction stage. At present, the comparison of spools is usually done in a manual manner in a CAD program or other software dedicated for this purpose and is implemented by combining variously defined translations and rotations. This approach is time-consuming and the results strongly depend on the survey engineer’s experience. In this article, a method of comparing the shape of two spools, based on isometric transformation and robust estimation, has been proposed. This method can be used to automate the comparison process. In standard approach, applied by both design engineers and assemblers, spools are described by a set of coordinates and, in the case of flanges, by sets of appropriately defined angular values. A method of flange description suitable for use in the isometric transformation process has been proposed, and potential problems that may appear at the implementation stage of the algorithm have been discussed. The proposed method makes it possible to determine the elements of a spool that do not fit into the design project in a way that allows minimizing the number of corrections at the construction stage.