Transformation to Continuous Cover Forestry (CCF) is a long and difficult process in which frequent management interventions rapidly alter forest structure and dynamics with long lasting impacts. Therefore, a critical component of transformation is the acquisition of up-to-date forest inventory data to direct future management decisions. Recently, the use of single tree detection methods derived from unmanned aerial vehicle (UAV) has been identified as being a cost effective method for inventorying forests. However, the rapidly changing structure of forest stands in transformation amplifies the difficultly in transferability of current individual tree detection (ITD) methods. This study presents a novel ITD Bayesian parameter optimisation approach that uses quantile regression and external biophysical tree data sets to provide a transferable and low cost ITD approach to monitoring stands in transformation. We applied this novel method to 5 stands in a variety of transformation stages in the UK and to a independent test study site in California, USA, to assess the accuracy and transferability of this method. Requiring small amounts of training data (15 reference trees) this approach had a mean test accuracy (F-score = 0.88) and provided mean tree diameter estimates (RMSE = 5.6 cm) with differences that were not significance to the ground data (p < 0.05). We conclude that this method can be used to monitor forests stands in transformation and thus can also be applied to a wide range of forest structures with limited manual parameterisation between sites.