We show that planar nanopatterned thin films on standard polycarbonate (PC) compact discs (CD) can be micro-shaped in a non-contact manner via direct e-beam exposure. The shape of the film can be controlled by proper selection of the e-beam parameters. As an example of application, we demonstrate a two-dimensional (2D) array of micro-lenses/reservoirs conformally covered by an Al 2D nanohole array (NHA) film on a PC CD substrate. It is also shown that such a curvilinear Al NHA layer can be easily transferred onto a flexible polymeric support. The presented technique provides a new tool for creating lab-on-CD architectures and developing multifunctional (flexible) non-planar nanostructured films and surfaces.