Looking at your script - it looks like you are trying to clear out a multi-value token.  I don't really understand why it is necessary to do that via a Script instead of just using an "Assign Token Values" activity to clear the token, but assuming you have a compeling reason  let's review your script.

When I create a workflow with two multi-value tokens, mainToken and otherToken, and pre-populate mainToken with some numbers (1, 2, 3, 4, and 5) and set it as an integer type token, and pre-populate otherToken with some numbers (1, 2, and 3) and set it as an integer type token, then add your script as you have listed it, I get the following errors:

So I tweak it as follows: change lines 4 to reference mainToken instead of unmainToken, add line 5 to declare the idx variable, and edit line 11 to include a space between end and if - script now looks like this: 

            Dim mainToken As List(Of Object) = Me.GetTokenValue("mainToken")
            Dim otherToken As List(Of Object) = Me.GetTokenValue("otherToken")

            dim maxCt as integer = mainToken.count()
            dim idx as integer = 0

            if otherToken.count() < MaxCt then
                for idx = otherToken.count() - 1 to (maxCt - 1)
                    otherToken(idx) = 0
                next
            end if

            SetMultiValueToken("otherToken", otherToken, false)

side note - using the "code" tags like this when posting makes it easier to read your code.

With those changes I don't get any errors and can publish, but when running the workflow, I get a message that the index was out of range.

In my example, the otherToken had a count of 3 and the mainToken had a count of 5, that for next loop is trying to run otherToken index 2 to 4 of the otherToken, but there is only 3 in there, so that's our index error.

I don't think I can get this code to work, because it's only running that loop if the otherToken count is less than the mainToken count, and then it's trying to loop through otherToken to the length of mainToken - which is always going to cause an index error, since otherToken had to be shorter to even get through the if statement and to the loop.

It would help if you provided a little more explanation regarding what the various tokens are used for, the situation if which you are trying to update them in the script, etc.