Formal definitions of nanotechnological devices for drug delivery typically feature the requirements that the device itself or its essential components be man-made, and in the 1-1000 nm range in at least one dimension [1]. The known nanovectors or nanostructures can be filled with drugs for different therapies and for diagnostical aims. Targeting moieties can also be attached to their surface. Polymeric nanovectors are generally made from biodegradable polymers such as polyesters, for example, poly-e-caprolactone (PCL). The drug delivery system known as nanocapsules (NCs) can be defined as a complex nanovector that is composed by a polymeric wall surrounding an oil core, where lipophilic drugs can be encapsulated. The advantages of NCs compared to other nanovectors are the high entrapment efficiencies of lipophilic drugs, low polymer content and low inherent toxicity. On the other hand, because of its complex blend of components NCs suspension allow several forms of nanovectors to be present at the same time, such as nanospheres, liposomes and nanoemulsions [2]. These ‘contaminants’ would be present in accordance with the type of formulation and method of preparation. Atomic force microscopy (AFM) has been used as a method for imaging the surfaces of liposomes [3] and nanospheres [4] allowing information in nanoscaled dimensions. In the present work, the NCs were prepared loading two different drugs, the antifungal albaconazole (ABZ), showing a crystalline drug structure and the antimalarial halofantrine (Hf) free base, having an amorphous form. These drugs possess high lipophilic character, which favours the association of the drug with the oily core, with drug loadings above 94%. Herein we studied the behavior of ABZ-loaded and Hf-loaded NCs through the AFM technique, searching to analyze and understand possible alterations induced by the drug inclusion in these nanostructures.