It looks like you may need to build up more paint in the touched up areas. As for smoothing things up, if you touch-up paint is lacquer-based, you can use product called Langka - it is not perfect, but it does help a bit. It will not work if your touch up is enamel paint - and being from hobby shop, it likely is.

In that case your other option is wet-sand with fine grits (1000-2000). Be sure to read about this procedure a lot if you decide to go this way, it is too easy to screw up paint! If you have clearcoated factory paint, your chances of success are higher, if it is just thin layer of base coat - you can easily rub through, and you will feel very sorry. After wet-sand you will have to polish with rubbing compound followed by fine polish to get rid of all fine scratch marks. If you do not feel confident, do not do it