Its abit tricky, depending where your Cylinder is.
If your Cylinder is below ground level, You can easliy place water in using air brushes, but bare in mind, that water continues throughout the whole level, depending how deep the water is.
You can try this....
Create a Sold Cylinder. Place an Air cylinder slightly smaller than the solid one. Go to the Brushes properties and tick "Is Portal" then Build Geomentry. Place the "Room Effect" object INSIDE the air cylinder and choose the Depth of the water.
Be careful, Portal type brushes are quite tricky when it comes to air brushes. They seem to spoof up quite alot in the editor and you may come across a hole in your map.
There will be a few glitches when using portals. They seem to like to create holes in your map, and also when you are looking at a portal through another portal, you can see your skybox. If you have no skybox, the place where the portal is will seem glitched out. Best route to go when using water is to put them in portals if you plan to have more than one body of water, or if you want water on an area that is not the lowest part of the map. (I'm back )
Imagine the glass part doesn't exist.. It is merely a decoration to go on afterwards, it will not hold water and as such will not help in the water being held there.
1. Make a solid cylinder and place it flush with the floor (v. important it is bang on the floor)
2. Insert an air cylinder, slightly smaller than your solid brush but keep the original height so it cuts the solid cylinder into a tube / pipe. Make this Air brush a Portal. This brush also has to sit flush with your floor.
3. Texture both these brushes with the sld_invisible.tga texture.
3. Now add your liquid room effect and it should fill with water.
4. You can now slip your glass detail brush around it, it shouldn't matter if it intersects with the solid brush as it has no bearing on how the water is contained.
In the pic you can see the Solid and Air brush described in steps 1-3. Make the glass cylinder brush by copy and pasting these 2 brushes, move them out of the way, uncheck "Is Portal" in the air brush's properties then select them both and hit Carve. Delete the air brush, texture the remaining solid brush with glass texture and then move it backinto position