We report a novel anisotropic process, termed plasma etching induced by temperature gradients (PE-TG), which we use to modify the 3D morphology of a hexagonally close-packed polystyrene sphere array. Specifically, we combined an isotropic oxygen plasma (generated by a plasma cleaner) and a vertical temperature gradient applied from the bottom to the top of a colloidal mask to create an anisotropic etching process. As a result, an ordered array of well-defined and separated nano mushrooms is obtained. We demonstrate that the features of the mushrooms, namely the hat size and their intrinsic undercut, as well as the pillar diameter and height, can be easily tuned by adjusting the main parameters of the process i.e. the temperature gradient and etching time, or the spheres' size. We show that PS mushroom arrays can be used as nanostructured templates to fabricate plasmonic arrays, such as gold-capped nano mushrooms and ultra-small nanoapertures, by using vertical and oblique gold sputtering deposition respectively. PE-TG reveals a new, cheap and facile approach to produce plasmonic nanostructures of great interest in the fields of molecular sensing, surface-enhanced Raman scattering (SERS), energy harvesting and optoelectronics. We study the optical properties of the Au-capped nano mushroom arrays and their performance as biosensing platforms by performing SERS measurements.