You can read the .xls file with xlsread in Matlab. Then you can organise the data into whatever will suit your purpose, e.g. removing or joining columns, or whatever else you need to do. Once you are satisfied with that, then simply use SAVE to save into .mat format.
If you already know the format you want for Matlab, you will probably find it easier to do the processing in Excel first, since you will already more familiar with that programme. In that case, simply use xlsread and then save the result.
You can also save the file from Excel as a CSV file, and you can use the Matlab Import tool to import that file into Matlab.