List

In[]:=
original={{{{36-72m^2},{-36},{9+8m^2}},{{4-2em-9m^2+3dm^2},{-4+em+dm^2},{1+m^2}}},{{{-40,32m,9+8m^2}},{{-5+5d,e+4m+dm,1+m^2}}}};

Suboptimal

In[]:=
firstLayer=Flatten/@original[[1]]​​secondLayer=Flatten/@original[[2]]​​result={firstLayer,secondLayer}
Out[]=
{{36-72
2
m
,-36,9+8
2
m
},{4-2em-9
2
m
+3d
2
m
,-4+em+d
2
m
,1+
2
m
}}
Out[]=
{{-40,32m,9+8
2
m
},{-5+5d,e+4m+dm,1+
2
m
}}
Out[]=
{{{36-72
2
m
,-36,9+8
2
m
},{4-2em-9
2
m
+3d
2
m
,-4+em+d
2
m
,1+
2
m
}},{{-40,32m,9+8
2
m
},{-5+5d,e+4m+dm,1+
2
m
}}}

Optimal

In[]:=
Flatten/@#&/@original
Out[]=
{{{36-72
2
m
,-36,9+8
2
m
},{4-2em-9
2
m
+3d
2
m
,-4+em+d
2
m
,1+
2
m
}},{{-40,32m,9+8
2
m
},{-5+5d,e+4m+dm,1+
2
m
}}}