The AFM-IR signal amplitude is proportional to the local pump beam intensity. Hence, the relative position of pump laser focus and the AFM tip apex and the pump beam focal spot size need to be kept constant during a measurement. This is the reason AFM-IR instruments are typically sample scanning instruments. The conventional prism based bottom illumination AFM-IR design is engineered to minimize the effect of scanning the prism on focus position and spot size: by using a normal incidence of the beam onto the angled side of the sample carrier, the beam is not refracted, ensuring it will go through the tip position even when moving the prism. When the prism is moved along the plane of incidence of the beam the optical path length inside the high refractive index material changes, leading to a change in the focal plane. This is usually compensated for in large range movements by moving the focusing lens along the beam path, so the focal plane remains at the surface of the substrate. In the machined Si carrier, no compensation of focal plane is needed while scanning, as the optical pathlength (< 0.5 mm) inside Si is negligible compared to the focal length of the focusing lens (> 20 mm). In contrast to the conventional prism sample carrier, normal incidence of the probe beam is not possible in the Si carrier. The beam is always incident at an angle other than 90° onto the faces of the machined grooves and the direction of propagation is thus changed at the air-Si interface. This means that scanning the prism laterally (along Y in Fig. ), orthogonal to direction of the grooves, will lead to a shift of the focus position. Using non-sequential ray tracing to model the intensity distribution at the surface of the Si sample carrier, we see that, indeed, when the sample is moved sideways (in a direction orthogonal to the direction of the machined grooves) by 50 µm, the focal spot moves by ~ 9 µm relative to the original position (see Figure ). However, when moving sideways by distances typically used for AFM imaging (see Figure ), the shift is much smaller (< 1 µm). In this more realistic scenario for AFM-IR imaging we see negligible intensity changes at the surface, which would be removed by typical AFM-IR postprocessing such as spectral normalization or calculation of band ratios. However, when moving larger distances (e.g., when switching between different sample locations), the beam pointing potentially needs to be readjusted. When varying the wavelength, the expected effect on the depth of penetration is observed (i.e., shorter wavelength leading to lower depth of penetration as in Figure ). The depth of penetration of the evanescent wave developed at two simulated wavenumbers are dp=722.8 nm for 1730 cm -1 and dp=663.4 nm for 1601 cm -1 . This is in good agreement with our calculations using (2). Changing the wavenumber has minimal effect on the intensity of the evanescent field at the surface (see Figure ). A slightly larger field intensity at the surface is observed for the higher wavenumber, which can be explained by slightly higher absorption in Si at the lower wavenumber. The evanescent field intensity at the surface is close to four times higher than the incoming field intensity. This intensity enhancement effect in total internal reflection close to the critical angle is well known (see the review of Martin-Fernandez et.al. for a theoretical discussion).