please use scatteredInterpolant, example:
a = randi([6 10],30,20);
a(randperm(numel(a),20)) = nan; % a - your 2d array with nan's
[r,c] = ndgrid(1:size(a,1),1:size(a,2));
l0 = ~isnan(a);
F = scatteredInterpolant(r(l0),c(l0),a(l0))
surf(a)
a2 = F(r,c);
figure,surf(a2)
