The amorphous Ti₅₀Ni₂₅Cu₂₅ alloy was subjected to high pressure torsion (HPT) processing. TEM studies revealed in the structure of the HPT-processed samples the presence of nanocrystals with a size of about 5 nm and amorphous clusters with a size of about 10-30 nm. Atomic force microscopy (AFM) was used to study the surface morphology of foils prepared by ion polishing from the initial amorphous ribbons and HPT-processed samples. AFM images of the foil prepared from the initial ribbon revealed a smooth surface with an average roughness of 0.3 nm. A totally different surface morphology was observed for the foil prepared from the HPT-processed state by the same regime of ion polishing: the presence of holes with a depth of 2-4 nm and a width of 10-30 nm. The changes in the surface morphology, namely the holes-like surface morphology of the HPT-processed state, could be explained by a complex transformation of the amorphous structure, and probably by the variation and redistribution of free volume, which leads to the emergence of a cluster contrast in TEM images.