How to close the holes by Iscocaps or other, the purpose of achieving a watertight geometry?

I have already capped the wall between the 2 intertwined volumes. This wall is where material will be filled in additive manufacturing (should I have capped/filled it? for Fluent to recognize as a wall, not a hollow space, when I do heat transfer simulations?). Now I need to close the remaining holes, and then mesh their faces for further simulation in Ansys Fluent. My current Fluent version takes only watertight geometry. I am not providing an executable code because there are many lines prior to this step. But you will be able to guide me from this stage.

[F1,V1] = isosurface(X,Y,Z,structure,0);
[F2,V2] = isocaps(X,Y,Z,structure,0);
%Combines isosurface and isocaps into one
F3 = [F1;F2+length(V1(:,1))];
V3 = [V1;V2];