@Courtney Navarre - since you have the handle s2 to the surf object that you replace on each iteration of the loop, then jusst delete this object after the timer expires. Something like
for i = 1:length(theta)
th = theta(i);
ang = th*pi/180;
x = (a/2) + r*cos(ang);
y = (b/2) + r*sin(ang);
z = c/2;
d = rand(1,37,'single');
e = ones(size(z))*d(i);
s2 = surf(x,y,z,e);
direction1 = [0 0 1];
rotate(s1,direction1,th)
direction2 = [0 0 1];
rotate(s2,direction2,2*th)
drawnow
pause(0.5)
delete(s2); % <---- delete the object here
end
