well don't say they are 2D or 3D shapes because that'll confuse everything...
I see what you're trying to get at though. You're right, when you draw BF3, all atoms are in the same plane, because that's the furthest the bonds can repel from each other, 120 degrees away, in a trigonal planar shape. When you look at CH4, the molecule is tetrahedral, there are 4 covalent bonds, no lone pairs of electrons. The bonds repel each other as far as possible, 2 bonds in the plane, one behind the plane, one in front of it. The angle between each bond is 109.5 degrees.
Now if you want to talk about lone pairs of electrons. A lone pair is a pair of electrons in a molecule, not involved in bonding. A bonded pair of electrons is the pair of electrons that are in a covalent bond. Remember, all a covalent bond is, is a pair of electrons. People tend to forget this, and a dative covalent bond, is a pair of electrons in a covalent bond, where the electrons are supplied from only one of the bonded atoms, not one from each like a normal covalent bond.
Think about a water molecule, H2O. The O is bonded to 2 hydrogen atoms, 2 covalent bonds. Then there are 2 lone pairs of electrons, these are unbonded. So the number of regions of electron density is actually 4. They repel each other as far as they can, but because a lone pair of electrons have a stronger repulsive effect than a normal bonded pair, they increase the bond angle by 2.5 degrees each.
So the bond angle instead of being 109.5 degrees like a tetrahedral molecule, is 109.5 - 5 or 104.5 degrees.
Hope that helps, feel free to ask more questions.