a b s t r a c t Infrared Microspectroscopy (IRMS) has been proposed as a powerful diagnostic tool in biology, due to the rich molecular, structural and conformational information contained in IR spectra of cells and tissues. In particular, IRMS of live cells in microfluidic devices has to cope with the strong water absorption in the medium infrared spectral region and the scarce knowledge about fabrication protocols suitable for micro-structuring infrared-transparent materials. Based on these motivations we are developing and testing a class of microfluidic devices consisting of a patterned photoresist sandwiched between two CaF 2 optical windows. In this paper we propose solutions to a few specific issues, namely, (i) the poor resist adhesion during micro-fabrication processes due to the low surface energy of CaF 2 , (ii) the potentially harmful effects of CaF 2 dissolution on interesting cellular lines (such as neurons or stem cells), (iii) the sealing of the devices. Specifically, we modified the surface properties of CaF 2 substrates by sputtering a thin layer of Si, as to obtain the following advantages: (a) all lithographic steps can be performed as if they were carried out on silicon wafers; (b) the chemical functionalization and nanostructuring of the surface in contact with cells can be obtained by usual protocols used for Si; (c) the deposited silicon separates living cells and their environment from CaF 2 . A device sealing process is discussed, based on a polymer bonding protocol, in order to tune the content of residual solvent. Finally, we present IR hyperspectral images acquired on MCF-7 living cells, cultured inside our devices for 48 h. Ó 2012 Elsevier B.V. All rights reserved.