Historical maps constitute an essential information for investigating the ecological and landscape features of a region over time. The integration of heritage maps in GIS models requires their digitalization and classification. This paper presents a semi-automatic procedure for the digitalization of heritage maps and the successive filtering of undesirable features such as text, symbols and boundary lines. The digitalization step is carried out using Object-based Image Analysis (OBIA) in GRASS GIS and R, combining image segmentation and machine-learning classification. The filtering step is performed by two GRASS GIS modules developed during this study and made available as GRASS GIS add-ons. The first module evaluates the size of the filter window needed for the removal of text, symbols and lines; the second module replaces the values of pixels of the category to be removed with values of the surrounding pixels. The procedure has been tested on three maps with different characteristics, the “Historical Cadaster Map for the Province of Trento” (1859), the “Italian Kingdom Forest Map” (1926) and the “Map of the potential limit of the forest in Trentino” (1992), with an average classification accuracy of 97%. These results improve the performance of classification of heritage maps compared to more classical methods, making the proposed procedure that can be applied to heterogeneous sets of maps, a viable approach.