Polarisation of light is a powerful and widely used degree of freedom to encode information, both in classical and quantum applications. In particular, quantum information technologies based on photons are being revolutionised by the use of integrated photonic circuits. It is therefore very important to be able to manipulate the polarisation of photons in such circuits. We experimentally demonstrate the fabrication by femtosecond laser micromachining of components such as polarisation insensitive and polarising directional couplers, operating at 1550 nm wavelength, where the two opposite behaviours are achieved just by controlling the geometric layout of the photonic circuits, being the waveguides fabricated with the same irradiation recipe. We expect to employ this approach in complex integrated photonic devices, capable of a full control of the photons polarisation for quantum cryptography, quantum computation and quantum teleportation experiments.