Well, presumably the excel file resides on the web server? If it does, and you have the Excel application also installed on the web server, then you can just use the Excel COM object library to do this, from your web app.
Well, do you know any Excel VBA? If you don't, then I suggest you use the macro recorder in Excel to record you opening a file and saving it to a certain path as CSV. Then have a look at the code the macro has created.
Once you've done that, you add a reference to the COM Excel object in your .net app, and use its Workbooks collection and Workbook object to manipulate the file in the same way as the macro code does.
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