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A clean install would be the best option to get rid of all the 'evil' traces on your partitions/disks. Of course before taking that step you'll have to take a backup of your documents, settings, installed programs, etc...
If you're not willing to go for the 'clean' option you can try with a tool like GParted
to resize the partitions so that everything is used by Linux. However, depending on the layout of partitions you have, you might encounter serious problems, forcing you to go for option 1, the clean install.
Last but not least you can just delete the partition table of the Windows partition and reformat it for Linux. After that just mount it on a mountpoint in your Linux and you're good to use it.