In the present work, the incubation effect on polycarbonate (PC) and poly(methyl methacrylate) (PMMA) foils has been investigated when irradiated with femtosecond pulses (400 nm in wavelength, 90 fs in pulse length and 1 kHz in pulse repetition rate). First, craters produced with different number of pulses (N = 1, 50, 100, 200 and 500) have been obtained and crater diameters measured by means of atomic force microscopy for single-shot craters (N = 1) and confocal optical microscopy for multi-shot craters. Taking into account the gaussian shape of the laser beam, the dependence of crater diameter with fluence has been well established according to a conventional description and, then, fluence thresholds extracted as function of the number of pulses. These values show a good agreement with the incubation model and the incubation coefficient, xi, has been obtained for both materials (xi = 0.68 for polycarbonate and xi = 0.61 for poly(methyl methacrylate)). This result supports well the observed fact that the incubation effects play a more important role in some thermoplastics than in any other kind of material, where xi usually lies between 0.8 and 0.95. In the second part of this work, these results have been considered in the machining of microchannels, since the. number of pulses is directly connected to the relative motion of laser beam and the sample through the feedrate of the stages. So, the observed broadening of microchannels with feedrate for a given fluence can be successfully explained and widths predicted with an uncertainty below 2 mu m. Finally, the channel depth is investigated and the well known transition between a gentle and a strong phase behaviour is showed in the case of polycarbonate. (c) 2006 Elsevier B.V. All rights reserved.