@Tatjana Mü: Simplify your view on the problem:
"So the idea is to import both files (which is working fine)" - than you can omit this part in the description, which mentions the Excel files. Start with some already imported data: "I have a cell array/table containing..."
"Later this files will have more than 30.000 lines." - then they are still small.
This is fragile:
filename=strcat(pfad,nur_file_name);
Prefer fullfile instead of strcat.
Instead of casting a scalar cell string to a CHAR, simply access the contents of the cell string:
% fid_in=fopen(char(filename(xy)),'r');
fid_in=fopen(filename{xy}, 'r');
You do this some linaes later, but fid_in is neither used nor closed. Simply omit the fopen line.
The text of the question until "This part is working fine" is not useful to solve your problem, but typing this has wasted your time only - and the time of the readers. In opposite to this, the explanation of the actual problem is really lean: "compare it and save the mineral names in the sample file".
Your "Datenbank" and "iwant" are string matrices or vectors? Then start with some Matlab code, which creates a tiny but relevant example and post a manually construted output.
