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A word of caution, if you are selecting all the vertices in a level to try and align things to the 64x64 grid in DeePsea, if you have the grid set at 64x64 all the vertices will snap to that setting.
This is both good and bad. Good, because all the teleports and so on will be aligned correctly, but bad because things that are not supposed to be will also be aligned to the 64x64 grid. eg a door or step that is only 16 wide will have its vertices snap to the nearest 64x64 point, and so its lines may end up lying on top of others and merge with them etc.
One way round the problem is to switch snapping off (/ key) toggle the grid to 64x64, select all the vertices you want to move and move one you know needs to be on a 64x64 corner to the correct point. Remember, no snapping will mean you need to be accurate (zoom in, + key) as you can move the vertices unit by unit. It will also mean that other vertices, whilst they will move correctly in relation to each other, will not snap to the grid, which may be something you need.
What you can do instead when moving a bunch of vertices is work out a point on the 64x64 grid that you want to use as a reference for the corner of a certain sector, keep your eye on it and toggle the grid down to something appropriate (2x2 is the smallest) and then move the appropriate vertex onto the correct location, all other vertices will move correctly with respect to each other. They will also snap to a 2x2 grid in this case, which will only cause problems if you have vertices closer than that.
Judging by another thread in these forums, the above method just got a lot easier because Jack has just implemented a grid display mode where the 64x64 lines/corners stand out more. So no having to keep your eye on the correct grid point when toggling the grid down to smaller values as there will be the option of having a coloured cross or something on the 64x64 line intersections.
Although, once you have realised that aligning levels to the 64x64 grid is important for specific flats, you are unlikely to need to fix whole levels like this again (presumably you will align appropriate sectors correctly in future) it is still a very useful thing to be able to do when you need to shift large structures around in a level. I find it particularly useful when I have pasted a lot of detail from a temporary working level or similar into another level.
Before moving a whole load of vertexes, you might want to change the vertex merge tolerance (in the map page of the DeePsea F5 preferences) to a nice low value, to stop close vertices merging in detailed maps.
Of course, Ezxariarch, you never said you were using DeePsea, so if you aren't, I'm sure you can just ignore the above unless there is something in it applicable to your situation.