Lets assume that I want to rename a file:
"topography_9x9._001.png" to "topography_9x9_001.png"
I would use
rename -n s/9\./9/g
topography_9x9._001.png renamed as topography_99_001.png
Why is the point not masked by the backslash?
You didn't quote the regex, so \
was interpreted by the shell:
$ echo rename -n s/9\./9/g
rename -n s/9./9/g
Quote your regexes:
rename -n 's/9\./9/g'