Focused ion beam micromachining provides a maskless and resistless technique for prototyping of structures from thermoplastic polymers, an example being the production of polystyrene microcantilevers with potential applications as micro/nanoelectromechanical systems sensors and actuators. The applicability of FIB technology is, however, often restricted by the damage created by high energy gallium ion bombardment and local beam heating, which can affect the desired properties and limit the minimum achievable size of the fabricated structure. To investigate the ion-induced damage and determine the limitations of the technique for polymer nanofabrication, we have exposed thin polystyrene film to the ion beam at varying ion doses, ion energies and specimen temperatures. Ion doses ranging from 10 16 to 10 18 ions cm -2 show significant gallium implantation, redeposition of sputtered material and chemical degradation in the polymer. Raman results show that the local heating in polymer during milling is severe at room temperature, damaging the aromatic carbon bonding (C = C) in particular. These observations are supported by the results of a beam heating model and Monte Carlo simulations. The chemical degradation caused by local beam heating is found to be significantly reduced by cooling the specimen to -25°C during milling. This is consistent with observations that reversible and repeatable thermal actuation of a fabricated polystyrene-platinum microcantilever is only observed when the cantilever is prepared at low temperature milling. Using this cooling approach, polymer structures can be fabricated with dimensions as low as 200 nm and still retain a sufficient volume of material unaffected by the ion beam.