Matlab prevents external program from accessing a file when Matlab script is running

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I am controlling Altair Hypermesh (FEA Program) using MATLAB . My workflow consists of initializing tcl scripts using the command prompt called by MATLAB. The command prompt will open Hypermesh and start the tcl script. One of the tcl scripts that I wrote uploads a file into Hypermesh (.fem file), which was previously edited with MATLAB. However, there is an error in Hypermesh which says that the file does not exist (but it does). This error only occurs if MATLAB is running a script. The .fem file is able to be manually uploaded with no errors only if MATALAB has stopped running.
I believe that the problem has something to do with MATLAB preventing Hypermesh from accessing the .fem file. The function fclose('all') was used to close all files but this does not solve the problem.
Is the source of the problem MATLAB or Hypermesh? My computer is Windows 10 Home edition, so perhaps it is an OS problem?
It would be great if I could receive any advice or solutions.
Thank you

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