Fruits and vegetables are built mainly of thin walled parenchyma cells highly susceptible to mechanical damage. According to experimental investigation of relationship between cells geometrical parameters and mechanical properties of tissue a new efficient method of structure reconstruction and parametrisation is elaborated and presented in this paper. Special sample preparation and way of image taking by Confocal Scanning Laser Microscope with fluorescence mode allows obtaining images of any number of cells. Unique computer procedure based on morphological operators was created that allows analysing automatically any number of images with extracting geometrical parameters of each cell separately. The method was tested on potato and carrot tissue. Results show that the method is fast and gives proper cell reconstruction for both materials. In order to decrease error of incorrect reconstruction, possibility of manual correction was introduced to the procedure.