In southern Australia, many native mammals and birds rely on hollows for sheltering, while hollows are more likely to exist on dead trees. Therefore, detection of dead trees could be useful in managing biodiversity. Detecting dead standing (snags) versus dead fallen trees (Coarse Woody Debris—CWD) is a very different task from a classification perspective. This study focuses on improving detection of dead standing eucalypt trees from full-waveform LiDAR. Eucalypt trees have irregular shapes making delineation of them challenging. Additionally, since the study area is a native forest, trees significantly vary in terms of height, density and size. Therefore, we need methods that will be resistant to those challenges. Previous study showed that detection of dead standing trees without tree delineation is possible. This was achieved by using single size 3D-windows to extract structural features from voxelised full-waveform LiDAR and characterise dead (positive samples) and live (negative samples) trees for training a classifier. This paper adds on by proposing the usage of multi-scale 3D-windows for tackling height and size variations of trees. Both the single 3D-windows approach and the new multi-scale 3D-windows approach were implemented for comparison purposes. The accuracy of the results was calculated using the precision and recall parameters and it was proven that the multi-scale 3D-windows approach performs better than the single size 3D-windows approach. This open ups possibilities for applying the proposed approach on other native forest related applications.