Nanoscale science is an emerging field of our time and opens a broad horizon for applications in almost every area of human activity, from medicine to energy storage. As usual, there are numerous challenges in the way of progress, which slow down the development and application of new ideas. Therefore the versatile investigation of nanostructures is of current importance for the realization of future technologies. The central aim of this thesis was to advance the field of molecular nanoscience on several crucial fronts. For that, the scanning tunneling microscopy (STM) was chosen as the principal experimental technique. It provides an unprecedented resolution at the atomic scale and can be used to reveal topographical or electronic properties of single molecules or atoms on conducting surfaces. Moreover, it gives a certain freedom to manipulate the object of interest at the nanoscale by the apex of the scanning tip. The introduction to this thesis gives a brief overview about the history of nanotechnology and its current status. In the first chapter the theory of the tunnelling effect and the working principle of the STM are presented and the experimental set-up is described. The second chapter is devoted to shot noise measurements with the STM. At first, the theory of shot noise is presented from the view point of the scattering approach. The challenges that arise on the way towards noise detection are discussed from two different sides: current and voltage amplification. Several test measurements are suggested for the approval of the amplification circuity. Afterwards, the data obtained on the copper and gold quantum point contact are shown. The third chapter presents an investigation of a purely organic radical with spin system 1/2. This molecule was previously studied on the Au(111) surface and demonstrated a Kondo effect in the weak coupling regime. In this thesis, its adsorption on Pd(111) and cobalt islands on Cu(111) is explored. The obtained data reveal electronic transport where molecular orbitals and vibration excitations are involved. The final chapter presents an investigation of the sequence controlled polymers - the oligo-triazole amide trimers, which were successfully deposited on the Cu(100) surface by means of the electrospray ion-beam deposition technique. The molecules show a large variety of adsorption conformations which are correlated with the sequence of monomers in the molecular backbone. Each chapter contains a summary and outlook, where possible improvements are discussed and future experiments suggested.