If you are using stlread to load the stl file, I suggest using one of the corresponding plot functions (trimesh, triplot, or trisurf).
See the Displaying Graphics in App Designer for more details on how different plotting functions are handled. For example
Specify Axes as Name-Value Argument
Some graphics functions require the target axes object to be specified as a name-value argument. For example, when you call the imshow and triplot functions, specify the axes object to display on using the 'Parent' name-value argument. This code displays an image on an existing set of axes on your canvas:
ax = axes;
data = stlread('BracketWithHole.stl');
trimesh(data,'Parent',ax,'EdgeColor','k')
