the windows have an exterior frame and an interior frame. the screws you see around the inside frame squeeze the two frames together when tightened. under the outside frame's lip is a bead of clay-like putty available from any RV-trailer supply joint. it comes in a tape form about an inch wide by maybe an eigth thick. compressing the two frames together with the screws squishes the putty tape forming the seal.
when taking a window out you should be able to remove the inner frame entirely; the outer will likely stick to a greater or lesser extent depending on how it has faired and how well it was installed initially. if you clean off all the old putty & reinstall perfectly you should get a small but variable amount of squeeze-out all around the exterior frame that can be trimmed neatly with a plastic knife so as not to scratch the paint.
Some add a thin bead of silicone over the top, some all around, after the bead is trimmed well. I don't recommend using silicone under the frame; it will glue in the frame & if you EVER have to remove it later, you will wish you used the putty.
Baja-tested '08 2-slide 36'
Alpine: The Ultimate DIY'er Project