Actually, do not use cd at all. It's a complete waste of time and may cause code to fail since it affects where matlab looks for m files. There is absolutely no point in changing the current directory to create a new directory, since, as you demonstrated yourself, mkdir accepts a parent directory (and if it didn't you could pass the full path of the directory to create anyway).
The root cause of your problem is that the 'VS' directories must be created in the loop, not after, and as subdirectories of the main directory you create in the loop.
New_Directory = fullfile(...
plasma_dir = fullfile(New_Directory, 'plasma');
Num_IDs = input('Enter the number of IDs: ');
for id = 1 : Num_IDs
iddir = input('Enter ID number: ', 's');
idpath = fullfile(plasma_dir, iddir);
mkdir(idpath, 'Vs L');
mkdir(idpath, 'VS O');