couresy of Matlab Tech Support-
The Model Explorer tree ordinarily does not show anything under a masked subsystem. However, once the user has forced open a masked subsystem by selecting "look under masks", the tree should start treating that masked subsystem as it would a normal subsystem.
The Model Explorer filters out objects that you usually do not navigate to. This would include masked subsystems. To view the contents within the masked subsystem in the Model Explorer, you would need to click the "Look Under Mask" option for the subsystem in your Simulink model. Once the first "look under mask" happens, the tree in the Model Explorer will start making that masked subsystem available. Any masked subsystems under that will remain inaccessible, unless and until you click "Look Under Mask" on one of those.
In the case that the Model Explorer still fails to show objects under masks after following the above procedure, please open your Model Explorer first then mask your subsystems. A possible procedure for this is to
1. Copy and paste the unmasked blocks into a new model, and watch the model tree in the Model Explorer, then
2. Mask the subsystem and add in any necessary parameters.
The objects/blocks under the masked subsystem should not disappear in the Model Explorer and your simulations should run fine.
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