The recent technological advances are producing huge data sets in almost all fields of scientific research, from astronomy to genetics. Although each research field often requires ad-hoc, fine tuned, procedures to properly exploit all the available information inherently present in the data, there is an urgent need for a new generation of general computational theories and tools capable to boost most human activities of data analysis. Here, we propose probabilistic principal surfaces (PPS) as an effective high-D data visualization and clustering tool for data mining applications, emphasizing its flexibility and generality of use in data-rich field. In order to better illustrate the potentialities of the method, we also provide a real world case-study by discussing the use of PPS for the analysis of yeast gene expression levels from microarray chips.