Proteins are large, complex macromolecules found in every cell and cell component and play a variety of roles essential to the body's functioning. There are four levels of protein structures, which can be classified as follows: primary, secondary, tertiary, and quaternary. Understanding the structure of proteins is often necessary to understand their biological processes. Several analytical techniques are commonly used to characterize the different structures of proteins. For example, X-ray crystallography, nuclear magnetic resonance (NMR), and electron microscopy (EM) are established techniques. Atomic force microscopy (AFM) is another imaging technique that can be used to characterize the nanoscale surface properties of materials. AFM's ability to produce images up to atomic-level resolution is one of its most significant advantages. It can also be used to examine a wide variety of materials, such as metals, semiconductors, polymers, and biological samples, and it can be used in a variety of environments, including air, liquid, and vacuum. Raman spectroscopy is a powerful analytical technique that identifies and studies the vibrational modes of molecules. Nonetheless, this Raman effect is a rare event, and proteins in the cell are present at extremely low concentrations, which contributes to the weak Raman signal. In order to improve the sensitivity and resolution of the method, scientists employ a technique based on the surface plasmon resonance effect, which increases the local electric field of the incident light and, consequently, the Raman signal (plasmon-enhanced Raman spectroscopy). When combined with the AFM technique, both high-resolution images and detailed chemical information can be retrieved, making this technique a highly effective method for characterizing protein structures. In this thesis, three levels of protein structures were characterized using AFM and plasmon-enhanced Raman spectroscopy.