You can generate a mesh using gmsh that would contain hexes, prisms and tetrahedrals. You can do transition from
hexahedral layer to tetrahedral layer through the layer of prisms.
N=2;
Point(1)={-1,-1,0};
bline[]=Extrude{1,0,0}{Point{1};Layers{N};};//prism region boundary
prism_surf[]=Extrude{0,2,0}{Line{bline[1]};Layers{N};};//prism region base (meshed with triangles)
prism_vol1[]=Extrude{0,0,1}{Surface{prism_surf[1]};Layers{N};Recombine;};//prism volume
tet_vol[]=Extrude{0,0,1}{Surface{prism_vol1[0]};Layers{N};};//no recombine, hence getting tet part
h_side[]={prism_vol1[3],tet_vol[3]};
hex_vol[]=Extrude{1,0,0}{Surface{h_side[0]};Layers{N};Recombine;};//recombine gives us hexes
prism_vol2[]=Extrude{1,0,0}{Surface{h_side[1]};Layers{N};Recombine;};//recombine gives us prisms
side1[]={prism_vol1[5],tet_vol[5]};//x=1
side2[]={hex_vol[0],prism_vol2[0]};//x=1
side3[]={hex_vol[3],prism_vol2[3],prism_vol1[4],tet_vol[4]};//y=1
side4[]={hex_vol[5],prism_vol2[5],prism_vol1[2],tet_vol[2]};//y=-1
side5[]={prism_vol2[4],tet_vol[0]};//z=1
side6[]={hex_vol[2],prism_surf[1]};//z=-1
Physical Surface(1)={side1[]};
Physical Surface(2)={side2[]};
Physical Surface(3)={side3[]};
Physical Surface(4)={side4[]};
Physical Surface(5)={side5[]};
Physical Surface(6)={side6[]};
//domain[]={hex_vol[1],prism_vol1[1],tet_vol[1],prism_vol2[1]};
Physical Volume(1111)={hex_vol[1]};
Physical Volume(1112)={prism_vol1[1],prism_vol2[1]};
Physical Volume(1113)={tet_vol[1]};
Save the above to the some_name.geo file and run "gmsh -3 some_name.geo". This should give you the mesh file that
you can later convert to Nektar++ xml format. After that you just need to insert initial/boundary conditions, exact solution, etc. I've used it for testing with discontinuous Galerkin Helmholtz solver and it didn't work, but
it maybe that the prisms are better supported in case of continuous Galerkin.