3D heritage documentation has seen a surge in the past decade due to developments in reality-based 3D recording techniques. Several methods such as photogrammetry and laser scanning are becoming ubiquitous amongst architects, archaeologists, surveyors, and conservators. The main result of these methods is a 3D representation of the object in the form of point clouds. However, a solely geometric point cloud is often insufficient for further analysis, monitoring, and model predicting of the heritage object. The semantic annotation of point clouds remains an interesting research topic since traditionally it requires manual labeling and therefore a lot of time and resources. This paper proposes an automated pipeline to segment and classify multi-scalar point clouds in the case of heritage object. This is done in order to perform multi-level segmentation from the scale of a historical neighborhood up until that of architectural elements, specifically pillars and beams. The proposed workflow involves an algorithmic approach in the form of a toolbox which includes various functions covering the semantic segmentation of large point clouds into smaller, more manageable and semantically labeled clusters. The first part of the workflow will explain the segmentation and semantic labeling of heritage complexes into individual buildings, while a second part will discuss the use of the same toolbox to segment the resulting buildings further into architectural elements. The toolbox was tested on several historical buildings and showed promising results. The ultimate intention of the project is to help the manual point cloud labeling, especially when confronted with the large training data requirements of machine learning-based algorithms.