Remove permissions on a sharepoint sitecollection - sharepoint-2010

Question

So I have a list of sitecollections and with them everyone who have access to the sitecollections. A ; separated csv file, formated like /sites1/sites;AD\User1.
We need to make a cleanup on ~400 sites where we want to remove users beloning to a certain company or being in a certain AD.
I have this information so thats not a problem.
Is there a way to make a powershellscript to remove theese users on theese site collection, in the other output we don't have any list of where they have permission only that they have it somewhere on the site.
I would also need the output format in a good way so we can restore them in a case it would be needed?
Can this be done?
We used below to get the list of users:
$ver = $host | select version
if($Ver.version.major -gt 1) {$Host.Runspace.ThreadOptions = "ReuseThread"}
if(!(Get-PSSnapin Microsoft.SharePoint.PowerShell -ea 0))
{
Add-PSSnapin Microsoft.SharePoint.PowerShell
}
$pathSave = "D:\Script\Output.csv"
$pathRead = "D:\Script\\sites.txt"
write-output = "======================================================================="
[System.Collections.ArrayList]$objectCollection = #();
[System.Collections.ArrayList]$allUsersArray = #();
foreach($line in Get-Content $pathRead)
{
$site = Get-SPSite($line)
$sitecntr = 0;
#write-output " ";
write-output $site.Url;
$allusers = $site.RootWeb.AllUsers;
foreach ($user in $allusers)
{
if (!$user.IsDomainGroup)
{
$sitecntr++;
$outstring = $site.Url + ";" + $user.UserLogin + ";" + $user.Email
$a = $allUsersArray.Add($outstring);
}
}
$outString = "Totalt: " + $sitecntr
if ($sitecntr -ne 0) {
write-output $outstring;
write-output " ";
}
$site.Dispose();
}
write-output ""
write-output "Exporting to csv..."
Out-File -FilePath $pathSave -InputObject $allUsersArray
write-output "Finished! "
write-output ""

Answer 1

This script will ensure reader permissions to the specified user across the site collection.
**Keep in mind:** This is not the right way to deal with permissions issues!
$site = Get-SPSite -Identity "http://mysite/"
$user = Get-SPUser -Identity "mydomain\myuser" -Web $site.RootWeb
$assignment = New-Object Microsoft.SharePoint.SPRoleAssignment($user)
$role = $site.RootWeb.RoleDefinitions[[Microsoft.SharePoint.SPRoleType]::Reader]
$assignment.RoleDefinitionBindings.Add($role);
foreach ($web in $site.AllWebs) {
if ($web.HasUniquePerm) {
$web.RoleAssignments.Add($assignment)
}
}
Note: You need to be Site Collection Admin to use this script.