Just remove the undesirable equations and variables:
Clear@"`*";
diffFormula = (T[i + 1, k] - 2 T[i, k] + T[i - 1, k])/x^2 +
(T[i, k + 1] - 2 T[i, k] + T[i, k - 1])/y^2 == 0;
NP = 5;(*number of grid points*)
x = y = 0.05;
Table[T[0, k] = 325., {k, 0, NP}];
Table[T[i, NP] = 325., {i, 0, NP}];
Table[T[i, 0] = 325., {i, 0, NP}];
Table[T[NP, k] = 325., {k, 0, NP}];
inner = {T[2, 2], T[2, 3], T[3, 2], T[3, 3]};
eq = Flatten[Table[diffFormula, {i, 1, NP - 1}, {k, 1, NP - 1}]];
selectedeq = Select[eq, Count[#, Alternatives @@ inner, Infinity] < 2 &];
var = Flatten[Table[T[i, k], {i, 1, NP - 1}, {k, 1, NP - 1}]];
selectedvar = Complement[var, inner];
(# = 400) & /@ inner;
solution = Flatten@Solve[selectedeq, selectedvar];
s = Table[T[i, k], {k, 0, NP}, {i, 0, NP}] /. solution;
ListPlot@s
BTW, though the region you're dealing with is luckily simple, handling irregular region with FDM can be really frustrating. This postThis post is an example. If FDM isn't necessary for you, have a look at the FEM capabilities of NDSolve
new added in v10.