Forests can be efficiently monitored by automatic semantic segmentation of trees using satellite and/or aerial images. Still, several challenges can make the problem difficult, including the varying spectral signature of different trees, lack of sufficient labelled data, and geometrical occlusions. In this paper, we address the tree segmentation problem using multispectral imagery. While we carry out large-scale experiments on several deep learning architectures using various spectral input combinations, we also attempt to explore whether hand-crafted spectral vegetation indices can improve the performance of deep learning models in the segmentation of trees. Our experiments include benchmarking a variety of multispectral remote sensing image sets, deep semantic segmentation architectures, and various spectral bands as inputs, including a number of hand-crafted spectral vegetation indices. From our large-scale experiments, we draw several useful conclusions. One particularly important conclusion is that, with no additional computation burden, combining different categories of multispectral vegetation indices, such as NVDI, ARVI, and SAVI, within a single three-channel input, and using the state-of-the-art semantic segmentation architectures, tree segmentation accuracy can be improved under certain conditions, compared to using high-resolution visible and/or nearinfrared input.