A common method for dealing with non-flat geometries is the Proximity Force Approximation, which in effect assumes an effective Casimir interactions between locally parallel pairs on points on the two surfaces, and sums over all such pairs.
For a sinusoidally corrugated plate:
"Demonstration of the Nontrivial Boundary Dependence of the Casimir Force,"
A. Roy and U. Mohideen, Phys. Rev. Lett. 82, 4380 (1999)
Integrate over all configurations of the field in the space between deformed plates (or other boundaries)
Thermal fluctuations: Scalar field with Dirichlet boundary conditions
Quantum fluctuations: EM field is equivalent to Dirichlet + Neumann in certain geometries,
TM modes (Dirichlet) + TE modes (Neumann)
"Probing the Strong Boundary Shape Dependence of the Casimir Force,"
T. Emig, A. Hanke, R. Golestanian, and M. Kardar, Phys. Rev. Lett. 87, 260402 (2001)
(Non-perturbative "reduced distance" limit)
A sideways force to "align" the two plates at b=λ/2 :
Comparison with the result of pair-wise summation:
"Demonstration of the Lateral Casimir Force,"
F. Chen, U. Mohideen, et. al , Phys. Rev. Lett. 88, 101801 (2002)