We have an issue with some bases spawning semi underground. I have "Maximum Elevation Level":  set to 3.5 would reducing this help or would i need to adjust something else? 

In the profile file (/oxide/data/RaidableBases/Profiles/ ) try changing
"Option": "height",
"Value": "1.0"   <---- Change this value
This works most of the time.
Remember to reload the plugin after doing this

if your max elevation level is too high then you might be having some spawn on steeper hills.
if its the same bases all the time, then its a height seating issue, either as rustbot says, just change that for those bases, or, paste them down and re-copy them at the correct level. eye-level at the foundation floor. either way is changing the same value, if its easy, defintly worth recopying. yea its so sad getting chests underground, i cant even bring myself to take the cahnce on them, as a player.

I reduced it and it seemed to help a little i may reduce it some more we have a very rocky map so that could be part of the issue.

this is a duplicate thread

https://umod.org/community/raidable-bases/32739-spawning-mostly-underground?page=1#post-2

this fixes a bug introduced in 1.5.3. you may have to re-edit heights for bases not copied at the proper height