hi chris.... what u r telling is that when u create cylinder in top viewport, it looks like flat disc. In the top viewport it will look flat but u have to see other viewports too simultaneously and the main viewport is the perspective. if u have enlarged the top viewport then u'll see the flat disc.

Another Alternative- if u just clicked on the cylinder and drag it in the top , u will 1st drag and draw a circle... then u have to leave the mouse and move the mouse upwards to give it some height...or u can also modify it from the Parameters list.
think this will help.

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