Method and system for manufacturing of three dimensional objects comprising of base substrate (18) placed on the supporting plate (30), electron beam gun (2), feed means (17) for feeding of feedstock material to melting zone, positioning system (31, 36) for positioning of said supporting plate (30) with base substrate (18), vacuum tight operating chamber (29), wherein an energy source for generating of molten pool on the substrate and for melting of feedstock material in said system is gas-discharge electron beam gun (2) with cold circular cathode (8) placed between two circular anodic electrodes placed coaxially to said cathode (8) which generates electron beam (9) in the shape of hollow inverted cone, and feedstock guide (17) is placed along the axis of said of said electron beam gun (2), and said gas- discharge electron beam gun (2) and said feedstock guide (17) are combined in one functional assembly.