Selecting specific data from several columns

Hello, I really need your help with something. I attached a photo so it would be easier to explain. I have around 5000 different excel files, each of those files consist of 2 columns - title and value. As an example I put three of those files next to each other to show you what I need to do with them. As you can see I painted the first set of columns (title and value) green, it means that from each of of those 5000 thousand files I need only the rows that are in the green field, because later I will have to count specific averages and so on. For example, from another 2 files I don't need animal proteins, plant proteins, aminoacids. The problem is that not every file has the same number and order of the rows and I can't just put all 5000 files in one work sheet and delete the rows that I do not need. I know this is very hard to understand but I don't know how else to explain it. If any of you understood what I meant and have any ideas what I could do I'd be really grateful.
Screenshot 2019-11-07 at 18.15.48.png