The effects of fixation and dehydration on the distribution of heme-based molecules inside red blood cells and the structural integrity of the cells have been investigated using Raman mapping and AFM topographic imaging. A strong correlation was observed between the thickness of the cells as determined from AFM images and the intensity of the characteristic heme bands in the Raman maps, demonstrating that heme compounds are relatively evenly distributed inside dried and fixed cells in the majority of cases. The exception occurred when cells were dried in phosphate buffered saline, where more hemichrome appears close to the periphery of the cell despite the AFM image showing a plateau like topography. Using neat formaldehyde solution as a fixative is inadequate for a complete structural preservation and results in diffusion of hemoglobin into the surrounding area. However, a mixture of formaldehyde (3%) and glutaraldehyde (0.1%) in buffer was found to be sufficient to retain the structural integrity of cells with minimal autofluorescence. This protocol was also suitable for red blood cells infected with Plasmodium falciparum parasites, and preserved the characteristic knob-like structures on the infected red blood cell surface.