snow modelling using raster data with different resolution
To make sure I'm understanding correctly: You need to reproject some data from one coordinate system to another. Then you need to interpolate or resample it onto a grid.

If you are already familiar with MATLAB, then you can certainly use MATLAB. Look to the Mapping Toolbox for coordinate transforms (although it does not make life easy IMHO), and check out griddedInterpolant and scatteredInterpolant and their options for interpolation.

If you're more tool-agnostic it might be easier in R (check out the spatial, raster, and rgdal packages). Or, depending on your GIS system, there is probably a way to script or automate it there so that you do not have to work through the process manually for all your files.