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MultiTasking

I have written an application that has to process about 30,000 files from hard disk, and write a new file for each one processed.  What happens is that it tends to lock up IExplorer, WExplorer, and other components on Win98 system until it has completed (usually about 15 minutes)  Is there a workaround it make it maybe run longer, but free up resources?
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Thanks for your help!
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