One of the threats that has a significant impact on the conservation status and on the preservation of non-forest Natura 2000 habitats, is secondary succession, which is currently analyzed using airborne laser scanning (ALS) data. However, learning about the dynamics of this phenomenon in the past is only possible by using archival aerial photographs, which are often the only source of information about the past state of land cover. Algorithms of dense image matching developed in the last decade have provided a new quality of digital surface modeling. The aim of this study was to determine the extent of trees and shrubs, using dense image matching of aerial images. As part of a comprehensive research study, the testing of two software programs with different settings of image matching was carried out. An important step in this investigation was the quality assessment of digital surface models (DSM), derived from point clouds based on reference data for individual trees growing singly and in groups with high canopy closure. It was found that the detection of single trees provided worse results. The final part of the experiment was testing the impact of the height threshold value in elevation models on the accuracy of determining the extent of the trees and shrubs. It was concluded that the best results were achieved for the threshold value of 1.25–1.75 m (depending on the analyzed archival photos) with 10 to 30% error rate in determining the trees and shrubs cover.