In this study, multilayered films of polyethylenimine/poly (sodium-p-styrene sulfonate) (PEI)/(PSS) and type I collagen/heparin sodium (COL)/(HEP) were fabricated using the layer-by-layer technique, and fully characterized using Infrared Variable Angle Spectroscopic Ellipsometry (IRVASE) to simultaneously analyze the chemistry, thickness, and roughness of the multilayers with respect to changes in pH of the washing solution, and changes in temperature. Film topography and Young’s modulus were obtained by atomic force microscopy (AFM) and nanoindentation. Our results show that with IRVASE it is possible to analyze the thickness of the multilayers prepared using a washing solution of pH 5, obtaining values of 71.7 nm and 40.3 nm for three bilayers of PEI/PSS and COL/HEP, respectively. Film roughness varies between multilayer systems, obtaining values of 37.76 nm for three bilayers of PEI/PSS and 33.58 nm for three bilayers of COL/HEP. Increasing the pH of the washing solution for PEI/PSS yielded thinner films that were less susceptible to thermal induced changes in film chemistry in the range of 25 – 150 °C. PEI/PSS films decreased in thickness with increasing temperature up to 75 °C, whereas above 75 °C film thickness increased. Through IRVASE, a transition temperature for the PEI/PSS multilayers was observed at 75 °C. Temperatures above 37 °C drastically alter the chemistry and the thickness of the COL/HEP multilayers indicating a possible degradation of the polymers. We obtained, through nanoindentation, a Young’s modulus of 15000 kPa and 9000 kPa for 12 bilayers of PEI/PSS and COL/HEP, respectively. These results demonstrate that, using IRVASE, we can simultaneously evaluate the physical, chemical, and thermal properties of synthetic and natural multilayered polymeric films.