Can I eventually erase windows and have a clean hard drive?

[shnk]

Yes, you are right. Just format it using Windows tool.

Is it possible to directly delete from external harddisk?
I found that I cannot do the same within windows as most of the files are system files.
Is it wise to delete files by booting from Linux?
I do not want to format my external drive because it has large amount of data (800 GB), and I do not have spare hard drive to make its backup.