From the .f06 file description:
This is the main Nastran output file. It contains
the results of your analysis such as displacements
and stresses. It is in ASCII format so it can be
viewed in any text editor. It also contains
warning messages, error messages, and diagnostic
messages to help the user evaluate the quality of
the analysis results.
It is a text file that could be opened with textscan(), importdata(), and the like. What function are you using? From your post I am guessing you are reading it as binary data. Another possibility is that the text file and Matlab are using different encodings, so you could check for that.
I have never worked with Nastran, but I imagine that there will be some structure to how the text data is stored. Then you would need to pass the proper arguments to your import function.
If your question is how can I automagically import .f06 data to Matlab then then answer is you can't (as far as I know, but you could always look in the file exchange). I am afraid some effort might be required.