We present a comparative microscopic study on metallic templates prepared by nanosphere lithography. Scanning electron microscopy, low kV Energy dispersive X-ray spectroscopy, scanning ion microscopy, atomic force microscopy and confocal Raman spectroscopy were used to analyse the assembly of the nano-templates. Contact angle measurements allowed us to optimise the surface treatment of the Si substrate to obtain maximal spreading and regularity of the nanosphere arrays. After metal deposition and toluene nanosphere removal, we found the expected interstitial triangular structures, originating from the 2D single layer hexagonal sphere array. We also detected a number of other features such as rings, circles, cups and lines which were found to be generally positioned below the nanospheres. A review of proposed mechanisms and the various analysis performed here indicate that some of these features are partly polymeric and partly caused by residual material leaching out of the nanospheres at various stages of the process.