It would help to have the data, or at least a representative sample of it.
Without knowing more, I would create a grid over the dimensions of the (x,y) plane that included all those data, so the minimum of both the x-coordinates to the maximum of the both x-coordinates, and the same of the y-coordinates. You can create those grids using the ndgrid funciton. Then create surfaces of the data using the scatteredInterpolant function, and then use the ndgrid results to plot them.
That might go something like this --
x1 = linspace(1, 2, 10);
y1 = linspace(2, 3, 11);
z1 = randn(numel(x1), numel(y1));
x2 = linspace(2, 4, 12);
y2 = linspace(1, 5, 10);
z2 = randn(numel(x2), numel(y2));
[X1,Y1] = ndgrid(x1, y1);
figure
stem3(X1, Y1, z1, 'filled')
grid on
xlabel('X_1')
ylabel('Y_1')
zlabel('Z_1')
title('Data Set #1')
[X2,Y2] = ndgrid(x2, y2);
figure
stem3(X2, Y2, z2, 'filled')
grid on
xlabel('X_2')
ylabel('Y_2')
zlabel('Z_2')
title('Data Set #2')
FZ1 = scatteredInterpolant(X1(:), Y1(:), z1(:), 'nearest', 'none');
FZ2 = scatteredInterpolant(X2(:), Y2(:), z2(:), 'nearest', 'none');
x3 = linspace(min(min(x1),min(x2)), max(max(x1),max(x2)), 20);
y3 = linspace(min(min(y1),min(y2)), max(max(y1),max(y2)), 20);;
[X3,Y3] = ndgrid(x3, y3);
Z1i = FZ1(X3, Y3);
Z2i = FZ2(X3, Y3);
figure
stem3(X3, Y3, Z1i, 'filled', DisplayName='Z1i')
hold on
stem3(X3, Y3, Z2i, 'filled', DisplayName='Z2i')
hold off
grid on
legend(Location='best')
xlabel('X_3')
ylabel('Y_3')
zlabel('Z_3')
title('Data Sets Combined')
Much depends on your data and the result you want.
.
