In this article, two approaches are presented dealing with common challenges of two-dimensional boundary layer measurements with hot wire anemometry under challenging test conditions. Novel procedures for accurate determination of the sensor position and correction of the wall heat effect were developed and tested at high freestream velocities of about M1 = 0.3 and thin boundary layers (δ99 = 0.7 − 3.5 mm) of different transitional state in a low-density environment. First, a novel procedure for automatized determination of the accurate hot wire sensor position relative to the wall is presented. The quantification and correction of possible subminiature sensor misalignments is achieved by taking advantage of the linear nature of the laminar sublayer of each boundary layer. The statistical approaches for identification and verification of the linear sublayer demonstrate satisfying results of minimized position uncertainties of about 24 μm. Second, a highly adaptable method for correction of the well-known wall heat effect is presented. In contrary to a series of static correction approaches, the biased velocity information is corrected by optimizing the parameters of an exponential approach, where the correction term is optimized for each boundary layer individually. This novel approach resolves the problem of the limited applicability of static correction methods, caused by system inherent measurement uncertainties.