Hi there Velj,
You should not need to remove the EEPROM from the Main Unit.
The 3M Clips will work just fine....
Probably the best thing to do is list exactly what you have (In terms of EEPROM programmer and Software),
what you have done so far, and what exactly is happening....
Remember, there is no such thing as TOO MUCH information, and we cannot see what you have, or what you have done...
So its best that you try and convey this information so as everyone understands what exactly where you are stuck, and how they might be able to help...
(Typically a one liner for stuff like this is not enough information

)
The problem here is that there are literally thousands of different EEPROM programmers than you could be using...
Adding to this that for many EEPROM programmers, there are multiple software packages that can be used, different software and driver versions, and even Operating Systems (Linux, Mac, Windows XP, Windows 7)....
You get the idea....
With the information above, it would be anyone's guess what the cause could be...
It definitely sounds like that you wont be able to read or write from the EEPROM if you cannot get the programmer working...
Post up much more information as stated above, and we will try our best to help you out...
Otherwise, I would be going back to the person that sold you the EEPROM programmer, to try and work out what is going on there...
Hope this helps...