I committed several file changes without adding some files to .gitignore that I didn't want to include.
I added those files to .gitigonre (.npy and few .png)file and committed but files didn't remove.
How can I remove these files from all commits? if not possible from all commits I'm happy to a new fresh but a clean commit.
If you are fine removing commit history then simply delete those files which you didn't wanted to include and make another commit.
Once done, rebase all commits (Avoid this step if you don't want to clear commit history).
Add those files to .gitignore
to avoid pushing them again.
Steps you should follow for adding files to .gitignore
1) Add files which you don't want to commit in .gitignore
file
2) Commit .gitignore
file and push the changes
Next time, you won't see any of those file while making a new commit.
Let me know if you still face the issue!