I have a txt file with values like this:
3.6.4.2
3.6.5.1
3.6.5.10
3.6.5.11
3.6.5.12
3.6.5.13
3.6.5.2
3.6.7.1
3.6.7.10
3.6.7.11
3.6.7.2
3.6.7.3
Based on your example this will work. If you should somehow end up with examples like 3.6.5.02 and 3.6.5.2, then this code will not work.
@echo off
setlocal EnableDelayedExpansion
for /F "tokens=1-4 delims=. " %%G in (FILE.TXT) do (
set N=0%%J
set SORT[%%G%%H%%I!N:~-2!]=%%G.%%H.%%I.%%J
)
for /F "tokens=2 delims==" %%N in ('set SORT[') do echo %%N
pause