Direct assessment of forest regeneration from remote sensing data is a previously little-explored problem. This is due to several factors which complicate object detection of small trees in the understory. Most existing studies are based on airborne laser scanning (ALS) data, which often has insufficient point densities in the understory forest layers. The present study uses plot-based terrestrial laser scanning (TLS) and the survey design was similar to traditional forest inventory practices. Furthermore, a framework of methods was developed to solve the difficulties of detecting understory trees for quantifying regeneration in temperate montane forest. Regeneration is of special importance in our montane study area, since large parts are declared as protection forest against alpine natural hazards. Close to nature forest structures were tackled by separating 3D tree stem detection from overall tree segmentation. In support, techniques from 3D mathematical morphology, Hough transformation and state-of-the-art machine learning were applied. The methodical framework consisted of four major steps. These were the extraction of the tree stems, the estimation of the stem diameters at breast height (DBH), the image segmentation into individual trees and finally, the separation of two groups of regeneration. All methods were fully automated and utilized volumetric 3D image information which was derived from the original point cloud. The total amount of regeneration was split into established regeneration, consisting of trees with a height > 130 cm in combination with a DBH < 12 cm and unestablished regeneration, consisting of trees with a height < 130 cm. Validation was carried out against field-based expert estimates of percentage ground cover, differentiating seven classes that were similar to those used by forest inventory. The mean absolute error (MAE) of our method for established regeneration was 1.11 classes and for unestablished regeneration only 0.27 classes. Considering the metrical distances between the class centres, the MAE amounted 8.08% for established regeneration and 2.23% for unestablished regeneration.