I would like to know how to plot the boundary layer thickness using Fluent along the length of windtunnel into which the air enters from the inlet and exits from the outlet.

You can create an iso-surface that is at .99*inlet velocity. This surface will represent your BL. If you're looking for quantitative values of the BL height, then you can do an XY plot of the surface with the X axis being the flow direction and Y being the normal direction (if it's a CD nozzle or something where the wall height is changing, then you'll want to plot the height of the wall as well because you'll be looking at absolute space, not pure BL height).

Hope this helps, and good luck, Jason