Unable to receive the Energy Star Rating

It sounds like your building would fall under Case 2 Option 2. This path is available for buildings that aren't eligible for either an Energy Star rating or for Case 2 Option 1. You can use the Case 2 calculator, which is linked on the resources tab for this prerequisite, to determine if the building is eligible for Case 2 Option 1. If you're not eligible for Case 2 Option 1, then your best bet is to benchmark via Case 2 Option 2C and that involves using both the building's historic energy consumption and energy consumption from 3 comparable buildings to generate a benchmark for comparison.

I have the EXACT same issue, medical device plant. Where are we supposed to get energy consumption form 3 comparable buildings?

Manufacturing poses a substantial challenge for EAp2; there simply won't be any easy answers in most instances. As Ben notes, starting with the historic baseline comparison is the path of least resistance, but many buildings will not be able to document the required reductions in energy consumption (after normalizing for production) during the prescribed time period. In that case, two places you might look for comparable buildings are trade associations and the EIA, which collects manufacturing energy consumption data for a variety of product types in much the same way that they collect data for commercial buildings. It's not easy to make this work, but it can be done (and a number of plants have done it recently). Hope that helps, Dan