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. Nano-holes ablated at slightly above the threshold of ablation irradiance became nano-disks and nano-rings at slightly lower pulse energies. Subtle sub-1 nJ pulse energy control was harnessed to pattern large surface areas with controlled nano-alloying of Si and Cr. This technique is extendable to 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.