Recent technical and jurisdictional advances, together with the availability of low-cost platforms, have facilitated the implementation of unmanned aerial vehicles (UAVs) in individual tree detection (ITD) applications. UAV-based photogrammetry or structure from motion is an example of such a low-cost technique, but requires detailed pre-flight planning in order to generate the desired 3D-products needed for ITD. In this study, we aimed to find the most optimal flight parameters (flight altitude and image overlap) and processing options (smoothing window size) for the detection of taxus trees in Belgium. Next, we tested the transferability of the developed marker-controlled segmentation algorithm by applying it to the delineation of olive trees in an orchard in Greece. We found that the processing parameters had a larger effect on the accuracy and precision of ITD than the flight parameters. In particular, a smoothing window of 3 × 3 pixels performed best (F-scores of 0.99) compared to no smoothing (F-scores between 0.88 and 0.90) or a window size of 5 (F-scores between 0.90 and 0.94). Furthermore, the results show that model transferability can still be a bottleneck as it does not capture management induced characteristics such as the typical crown shape of olive trees (F-scores between 0.55 and 0.61).