Ultra-short 230 fs laser pulses of 515 nm wavelength were tightly focused into 700 nm focal spots and utilised in opening ∼400 nm nano-holes in a Cr etch mask that was tens-of-nm thick. The ablation threshold was found to be 2.3 nJ/pulse, double that of plain silicon. Nano-holes irradiated with pulse energies below this threshold produced nano-disks, while higher energies produced nano-rings. Both these structures were not removed by either Cr or Si etch solutions. Subtle sub-1 nJ pulse energy control was harnessed to pattern large surface areas with controlled nano-alloying of Si and Cr. This work demonstrates vacuum-free large area patterning of nanolayers by alloying them at distinct locations with sub-diffraction resolution. Such metal masks with nano-hole opening can be used for formation of random patterns of nano-needles with sub-100 nm separation when applied to dry etching of Si.