I like the option to Secure Overwrite files option in your program. I think there should be an option to Secure Overwrite MFT also in the program.
Check 'Wipe MFT Free Space' in Options/Settings. I believe that you have to have Wipe Free Space for that drive enabled, along with checking Wipe Free Space in Cleaner/Advanced. I understand that some users let Wipe MFT run then cancel Wipe Free Space, but as I don't use WFS I can't say how efficacious this is.
I was talking about Recuva. There is no such option available in Recuva.
Ah yes, I must have had a touch of moderator fever. No, it is not possible to overwrite MFT entries with Recuva. There is, as far as I know, no Windows API to do this. Recuva quite wisely does not hack into the MFT.
If it's a particular entry or group of entries you want to go then you could stop doing any temp file removal and keep your eye on the entry until it's overwritten (Recuva MFT listing, and Windows MFT record reuse, appears to be in ascending order), then start temp file removal again. If it's ad-hoc removal then Recuva is no help. As far as I know other MFT wipers work in the same way as CC.