In this chapter, we describe the submicroscopic structure analysis of isolated human amyloid fibrils (AA, AL and ATTR) by using different topo-optical reactions with polarisation microscopy. The fibrils showed the same properties as amyloid deposits in different organs after embedding. The protein (the P component), sialic acid, O-acylsialic acid, glycosaminoglycans and lipid components were analysed by using various specific topo-optical staining reactions. The reactions and reaction results agree with the results obtained in different organs with embedded amyloid material. According to our polarisation microscopic analysis, which included performing various staining reactions performed and analysing them with various topo-optical reactions, the fibrillar and nonfibrillar components of amyloid deposits have an ordered structure. Different components of the amyloid fibrils are linked in a highly oriented system.