We demonstrate the fabrication of a hybrid PDMS/glass microfluidic layer that can be placed on top of non-transparent samples and allows high-resolution optical microscopy through it. The layer mimics a glass coverslip to limit optical aberrations and can be applied on the sample without the use of permanent bonding. The bonding strength can withstand to hold up to 7 bars of injected pressure in the channel without leaking or breaking. We show that this process is compatible with multilayer soft lithography for the implementation of flexible valves. The benefits of this application is illustrated by optically trapping sub-wavelength particles and manipulate them around photonic nano-structures. Among others, we achieve close to diffraction limited imaging through the microfluidic assembly, full control on the flow with no dynamical deformations of the membrane and a 20-fold improvement on the stiffness of the trap at equivalent trapping power.