Aluminium nitride (AlN) films with different thicknesses (from 2.3 to 4.7 μm) were deposited onto high resistivity silicon substrates using magnetron sputtering. Crystalline and bonding structures of the deposited AlN films were characterised. The AlN films showed a highly c-axis texture. AlN film based surface acoustic wave (SAW) devices were fabricated and characterised. The SAW devices showed Rayleigh wave transmission band with a large side-lobe suppression of ∼15 dB. With the increase in film thickness, both the central band frequency and electromechanical coupling coefficient were increased, and values of temperature coefficient of frequency was increased linearly from −21.3 to −27.4 ppm/K. Microfluidic manipulations including streaming, pumping and jetting have been realised using AlN SAW devices. The applied RF power boundary between streaming and pumping and that between the pumping and jetting decreased with the increase of film thickness. The measured streaming and pumping velocities as well as device surface temperatures increased with the film thickness.