Surface contaminants, such as powder and thin film on various solid surfaces, were analyzed by ATR FT-IR microspectroscopy. An ATR accessory consisting of a miniature-Ge IRE with contact area smaller than 50 µm, in diameter was fabricated and employed for a non-destructive characterization. The IRE was pre-aligned and fixed onto a 15 × Schwarzschild-Cassegrain infrared objective. Easy maneuvering of the microscope stage enabled an accumulative collection of the contaminant at the tip of a miniature-Ge IRE, where the contaminants were analyzed under the ATR condition. By making a gentle contact between the Ge tip and selected area on the surface, any removable contaminants were transferred onto the Ge tip where its molecular information was acquired without any interference from the solid substrate. A thin organic film (i.e., mineral oil or fluorolube) was coated at the tip of the IRE in order to enhance the collecting efficiency of the removable contaminants.