Flat, Si-ATR. A flat, Si-carrier (Universal Single Reflection ATR Crystal, IRUBIS GmbH, Germany) with micromachined grooves on the backside was used in this work (cross section see Figure ). This ATR takes advantage of the grooves, allowing the IR-light to be coupled in the crystalupon which -there is a single bounce and subsequently an evanescent wave being formed at the surface. We will use the term 'slope' to refer to the angled, machined surfaces at the bottom of the chip throughout this work. The marked points of incidence (POI) IN1 and IN2 represent the parameters used for the simulation described later in this work. Figure shows a simplified schematic of the bottom-up AFM-IR setup utilizing the new carrier. The flat ATR is replacing the high-refractive index prism conventionally used (illustration see Figure ). The IR-beam is coupled in the crystal with an outer angle of incidence of 45°, so that the plane formed by the direction incident beam and the normal of the top surface is parallel to the micromachined grooves. Adaption of the AFM-IR system. The commercial AFM-IR system used in this work was originally optimized for ZnSe prisms. Thus, some adaptions were required to use it with flat sample carriers. This was achieved by using rapid prototyping technology (fused deposition modeling, FDM) to manufacture an adapted sample holder able to carry the flat Si carrier. The Si substrate is held completely flat on top of the sample carrier, fixed using Kapton tape or glue. This constitutes an additional advantage of our custom-designed sample carrier holder over conventional ATR holders which can introduce tilting of the top surface, which can affect AFM scanning.