The use of SU-8 photoresist as a structuring material for portable capillary-flow cytometry devices has been restricted by the near-hydrophobic nature of the SU-8 surface. In this work, we evaluate the use of chemical and plasma treatments to render the SU-8 surface hydrophilic and characterise the resulting surface utilising a combination of techniques including contact angle goniometry, atomic force microscopy and X-ray photoelectron spectroscopy. In particular, for low-power plasma treatments, we find that the chemistry of the plasma used to modify the SU-8 surface and the incorporation of O2 on that modified surface are paramount for improved surface wettability, whilst plasma-induced surface roughness is not a necessary requirement. We demonstrate a technique to obtain a hydrophilic SU-8 surface with contact angle as low as 7° whilst controlling and significantly reducing the level of surface roughness generated via the applied plasma. An additional chemical treatment step is found to be essential to stabilise the activated SU-8 surface, and incubation of the samples with ethanolamine is demonstrated as an effective second-stage treatment. Application of the optimised two-stage surface treatment to cross-linked SU-8 is shown to result in a smooth hydrophilic surface that remains stable for over 3 months. Copyright © 2015 The Authors Surface and Interface Analysis Published by John Wiley & Sons Ltd.