Well, it's not really possible to create a completely impregnable tower, but you can make a tower that is close enough. This assumes that you have an arbitrarily large amount of gold available, and that you are probably using the restoration XP loop. You can do without the XP loop, but this is not a cheap setup in terms of XP (lots of permanency and a wish).
First, you'll want to pick a suitably isolated spot. The top of a mountain should keep out anything that can't fly (and we'll deal with that below), so lets go there. Ideally, you want the top of the tower to be 20 feet wide, so plan for that.
First, construct the outer shell of the tower using wall of stone. Inside this, create a shell of permanent walls of force, layering them along the bottom as well. In between the outer and inner shells, place a layer of lead sheeting to block scrying, and line this layer with permanent alarms set to go off if anyone should breach the outer wall. On the outer wall, space auto-resetting traps of antimagic field so that the entire tower is surrounded by an antimagic field and conceal them as best you can. At the top of the tower, create a permanent prismatic sphere, and place an antimagic field traps on all four sides of the top of the tower, so that the prismatic sphere is completely encapsulated in an antimagic field. Inside, use a wish to emulate a forbiddance, filling the tower up to the prismatic sphere. Finally, place an auto-resetting trap of feather fall set to target you when you fall through the prismatic sphere inside the sphere.
That should cover the basics, and it's all Core too. Do this as a Red Wizard if you can, so you can Heighten the prismatic sphere to 20th level and ramp the CL for everything as high as you can.