If I draw a ball with black outline in one layer and then draw a center straight line dividing the ball into half on other layer. Then I do a flatten image just like in Photoshop. I was able to paint it in Photoshop but I was unable to do that in Animate Pro. Does that mean I have to close off the center dividing line in order to paint it?
There is in fact a flatten tool in Animate and it makes all of the strokes into a single stroke (right? I don’t use it much).
I gather from your post you have drawn a circle, put a line down the middle, and now you only want to pain half the circle but when you paint it still fills the entire circle even though you can’t see any gaps?
If that is the case try on the paint tool setting the close gaps to a larger setting.
I’m not certain exactly what you’re doing, because we don’t work like Photoshop. There’s no flatten. When you’re working in layers, there’s two types of layer - a drawing layer, which shows up as a new layer in your timeline. Then there’s also line art, colour art, underlay, and overlay that’s within one drawing layer.
What you probably want to do is draw your line on the line art layer, then select your line and do a “Create Colour ARt from Line Art” - which will take the strokes (outlines) from your line art and put them on your colour art. Then you can draw an additional stroke down the middle and colour it in. You can’t fill in a shape that isn’t closed, so that might have been your issue.
~Lilly
Oh oh I’m sorry yes there’s a Flatten in Animate of course - I was thinking of the Merge Layers - I’m sorry I got confused on that one.
Go to View > Show Strokes (K) and make sure there are no gaps in your line like TheRaider suggested. 
There I go again, trying to make things more complicated than they need to be…
~Lilly