Apparatus and methods for target detection in hyperspectral images are disclosed. In one embodiment, a method of detecting a target in a hyperspectral image includes spectrally unmixing the hyperspectral image into segments, each segment having at least one of similar spectral composition, similar textural composition, and similar variation, and spectrally unmixing at least one of the segments. The method further includes creating a clutter rejection filter for at least one segment, filtering at least one segment, and calculating target abundances in at least one segment. In alternate embodiments, channel reduction can be performed on the hyperspectral image and also on at least one segment. In further embodiments, data associated with the location of possible targets in the segments may be compiled. In yet another embodiment, this data may be compressed by cross referencing data from all segments and eliminating redundancies.