Apple does not provide an easy way to remove your epub files from the iBooks app, but it is possible. To convert from iBooks, you will first need to use a Computer to extract the epub files from your iOS Device, there’s a guide here:
Then simply drag the epub into the converter app using iTunes File Sharing (open iTunes > your device > scroll down to file sharing and the converter app). From there, just use the converter app to convert to mobi (for Kindle) or any other format you want.