You may specify a block to run only major time steps by specifying the sample rate as [0,1], signifying "Fixed in Minor Step". Also, refine factor data points can be created using the Configuration Parameter's option under additional parameters in the Data Import/ Export tab called "Refine factor". The solver will create Refined Factor -1 data points between the time steps.
However plotting only the Major and Refine Factor time steps is a limitation of the MATLAB system block, since a MATLAB system block is unable to discern the difference between minor time steps and the data points created from the refinement factor. One possible workaround is to use the "Run-Time Data Access" feature available when you right click on a logging badge and select properties. This will give you access to data as the simulation runs. This is found at the following link.
