During the first years, there is absolutely no need to cut a young citrus tree, since research has shown that any cut to a young tree reduces root growth. This is due to the equilibrium between the foliage and root system. A citrus tree is a biological unit. Cuts on a young tree, discourage canopy growth and delay trees coming into bearing. the only pruning on young trees should be to eliminate the central leader branch at about 30 inches . In some weak citrus varieties such as limes, satsuma, etc., it is not convenient to make any cuts at all. After a few years, DEPENDING on the speed of tree growth, climate and cultural practices, a very selective canopy thinning may be carried out. A two year old citrus tree should have been much taller than your tree was before you cut it. - Silica

Thank you Steve!! This is very helpful and I will do so ASAP!

Unless those two branches which appear to be 6 feet long are water sprouts gone wild, I think Jason is on target with the reason the tree is lanky. If you don't have a better window with direct sun for 5+ hours, you probably need to invest in some lights since it is an indoor tree, that is you only solution to get a viable more bush shape tree. I would light the tree - focus on the core - within 4 feet of the pot. When the stems bud out and form new branches and leaves (seems to take 2 months for me on new trees), then trim back the tree like Steve indicated.

Lots (which is not to say many, most, or all) are grafted, so look for the graft line if you can find it. Anything growing from under the graft line should simply be removed. Lemons do have thorns. Technically you can remove whatever you like at any time except when the lemon's flowering or fruiting (it removes energy from the plant at that time, which you don't want), although I tend to avoid heavy pruning during winter when I can on everything I can. Here, it's out of shape enough that I'd just do it. https://homeguides.sfgate.com/grow-pohutukawa-74987.html The link title is a bit off-putting but it talks first about lemons. In your case, I'd probably just neaten things a little and leave most of the height, really. It's a young lemon, it's going to grow. If you'd rather impose a bushier, shorter shape, though, that's certainly fine as long as it's not too forced.