Create grid
select any 5x5 region (25 faces), extrude | Region > +Y > 1 (say)
Select the middle 9 faces and extrude -Y > 0.5 say
(now got many thin 'walls' in this 3x3 area)
Select the verts at the tops of the 'walls' ... both in the middle of the mess and where the walls touch the sides (12 verts)
Move these -Y > 0.5 (or same as extrude op) or flatten Y rmb, use base of hollows as target.
(This makes the top verts co-incident with those that were at the bottom of the walls - in a way that Objcet cleanup can be used (so do that)
Re- connect the sloping / angled edges to themselves, then to the corner verts and re-align the top edges of the 'hollow' to get the orig. shape back (various ways of doing this Flatten rmb being one)
pp
edit
alternatively - for this grid based ex
assuming you've got the 9 hollows + walls
select the 9 faces at the base of the hollows
scale uni 50% say (amount irrelevant) - but helps to see what's happening / going on
Face | Flatten > Y > rmb (use top surface as target) ... or move -Y the same distance as the depth of the hollow (0,5 here)
Dissolve faces to re-form what you'd got at the beginning (select alternate middle faces - like the whites on a chess bd, + to enlarge seln, dissolve ... then do the others. If you do all 9 in one go you'll dissolve all into a single big face)
