The paper presents the results of an experimental study of the local polarization reversal and creation of domains by a biased tip of scanning probe microscope (SPM) in lithium niobate single crystals of congruent composition with a surface layer modified by soft proton exchange (SPE). The depth dependence of H$+$ ions concentration in the SPE-modified layer measured by confocal Raman microscopy demonstrates a sufficient composition gradient. The creation of isolated domains and stripe domain structures has been done by two switching modes: (1) point switching by field application in separated points and (2) line scanning switching by motion of the biased tip being in contact with the sample surface. For point switching for pulse durations less than 10$$s, the logarithmic dependence of the domain diameter on the pulse duration was observed. The change of the dependence to a linear one for pulse duration above 10$$s has been attributed to the transition from the stochastic step generation at the domain wall to the deterministic one at the domain vertexes. The periodical structure of stripe domains was created in SPE CLN planar waveguides by scanning at elevated temperature. The revealed switching regime suppresses electrostatic interaction of neighboring domains and leads to a significant improvement of the domain structure regularity. The creation of the stable periodical domain structure with submicron periods in SPE CLN planar waveguides was demonstrated.