How to remove unwanted vertexes inside mesh

Hi I got this problem every time and it’s gets laggy in the edit mode. I want automate this process with boolean operation in carve mode.
I seen this in stackoverflow and I don’t much about python and it will useful to everyone and with ctrl + shift +alt+m it gives non manifold vertexes and we can fill them with alt+for

i have uses this process to solve the problem but, it takes some time for small problem

1 enter edit mode
2 select edge mode
3 shift + ctrl + alt + m
4 deplicate
5 seperate them
6 exit edit mode and open seperated objects
7 again seperate them with loose parts
8 then again open them every single them and do alt +f
9 join them all and remove duplicate vertexes

see its a lot for small thing and it works perfectly with any type of object but if you have million then it gives you hard times. so i want simplify this with simple addon
separating object kinda stupid thing you thing( and im also thing its stupid but, if you have two holes at same from any direction its gonna bridge them. thats why i want to seperate them and fill every single object seperatly.

if any body now do this in a efficient way please help.