With the scanning tunneling microscope (STM) it became possible to perform controlled manipulations down to the scale of small molecules and single atoms, leading to the fascinating aspect of creating manmade structures on atomic scale. Here we present a short review of our work in the last five years on atomic scale manipulation investigations. Upon soft lateral manipulation of adsorbed species, in which only tip/particle forces are used, three different manipulation modes (pushing, pulling, sliding) can be discerned. We show that also manipulation of highly coordinated native substrate atoms is possible and demonstrate the application of these techniques as local analytic and synthetic chemistry tools with important consequences on surface structure research. Vertical manipulation of Xe and CO is presented, leading to improved imaging and even chemical contrast with deliberately functionalized tips. For the transfer of CO it is shown that beside tip voltage current effects play also an important role. This is also the case for the dissociation of molecules. With CO transferred deliberately to the tip we have also succeeded to perform vibrational spectroscopy on single molecules. Furthermore, first experiments aiming for the transfer of all manipulation modes to thin insulating films are described.