Subtractive femtosecond laser machining using multiple pulses with different spatial intensity profiles centred on the same position on a sample has been used to fabricate surface relief structuring. A digital micromirror device was used as an intensity spatial light modulator, with a fixed position relative to the sample, to ensure optimal alignment between successive masks. Up to 50 distinct layers, 335 nm lateral spatial resolution and 2.6 µm maximum depth structures were produced. The lateral dimensions of the structures are approximately 40 µm. Surface relief structuring is shown to match intended depth profiles in a nickel substrate, and highly repeatable stitching of identical features in close proximity is also demonstrated.