Conductive Tip AFM (CT-AFM) is commonly used for electrical characterization of organic and inorganic molecular surface systems. Understanding charge transport at the molecular level is of crucial importance for developing molecular assemblies with uncommon properties for novel applications, such as molecular electronic devices and sensors. Measurements of the charge transport at the contacts and through molecules will provide crucial insight into the electronic coupling within and between molecules and at the interface. From a more general point of view such studies aim at expanding our fundamental understanding of electron-transport processes, that is a central issue of biophysics and chemistry. In this work we follow an approach to the study of Metal-molecule-Metal surface junctions that uses a combination of different AFM-based techniques. We first use Nanografting to build nanopatches of the molecules of interest into a hosting reference self assembled monolayer (SAM) typically made of alkanethiols. After the tip is changed to a conductive one, CT-AFM is used to characterize electrically the whole system recording, at the same time, the system topography. Some of the advantages of this approach are the possibility to build and study a wide range of different monolayers side-by-side in a relative way, overcoming all the problems of an absolute measure, and the in-situ control of the quality both of the hosting monolayer and that of the grafted patches. Preliminary results demonstrating the reliability of the technique will be presented for alkanethiols spontaneously self-assembled and nanografted on Au(111) surfaces. Moreover, we will show that in the case of alkanethiol molecules of one specific length, i.e. C10, nanografted into a SAM carpet of the same molecules, a contrast in current images appears, that can be correlated to the higher quality of the molecular packing inside the nanopatches with respect to the surrounding SAM.