If I understand your question, you are having trouble reading mat files from SCIRun into Matlab and from Matlab into SCIRun.  We haven’t seen a problem with loading mat files from SCIRun into Matlab before, unless it is a large data format. It may be possible that you uncovered a bug.  You could create a github issue for this or further explain it here, but we would need an example file and a description (steps to reproduce it, and matlab, SCIRun and operating system version) of how you generated it.  

For loading mat data into SCIRun, it is possible through readfield, though it can be a bit tricky.  SCIrun will convert a matlab structure array (length of one) with fields that correspond to the SCIrun field properties.  The simplest geometry to import is a point cloud, and in this case the matlab structure will need to at least have a field for the node locations.  It needs to be named ‘pts’ or ‘node’ and should contain a matrix of 3xn or nx3 where n is the number of nodes. More field properties can be added as needed, such as field data (a field called ‘field’ containing an array of data of length n). A file with only this structure will load into SCIRun via the ReadField module, but if multiple structures are saved in one file you can try ImportFieldsFromMatlab.  If you have specific geometries and data that you are struggling with we can address those.  

cheers,

Jess