Bulk metallic glasses (BMGs) are well known for their promising properties. Surface properties can be further improved by using certain techniques such as electron beam melting (EBM), laser beam melting (LBM), ion irradiation, ion implantation and neutron irradiation. BMGs especially Zr-based BMGs have numerous applications as structural materials. In this manuscript, the results are presented on microstructural investigations and phase formations in Zr-based BMGs modified by using above mentioned techniques. Microstructure was studied by scanning electron microscopy (SEM). Phase analysis was done by X-ray diffraction (XRD) and confirmed by energy dispersive spectroscopy (EDS). Vickers hardness was measured and correlated with the microstructure. The phases identified in Zr-Cu-Al-Ni alloy samples modified by EBM, LBM and ion irradiation are Ni-Zr, NiZr2, CuZr2, Cu10Zr7 and Al2NiZr6. ZrSi2 phase was detected in Zr55Cu30Al10Ni5 and Zr65Cu17Ni10Al8 BMGs irradiated with Si+ (ions). About 20-35 % increase in hardness and elastic moduli was achieved by surface modification. Modifications of BMGs by electron and laser beams melted the materials surfaces while ion irradiation improved the mechanical properties of localized zones without melting.