My younger brother spoiled my laptop with pens. On removing the stains I got marks on the surface of the laptop which make it look dirty. Are spray paints effective for painting laptops or is there any other way to deal with it?
No, spray paints can get into the cooling system through the vents, blocking air flow and gumming up moving parts. Some spray paints may even conduct electricity after drying which can short out (seriously damage/destroy) your laptop's electrical components. The only "safe" way to use spray paint on any electrical device is to unplug (remove battery) and dismantle it, removing the electronic components from the outer shell. Then paint just the outer shell in a non-conductive paint before reassembling the device. Since laptops use lots of springs and pressure fitted parts, the dismantling process itself is another great way to destroy a laptop, so don't do it.
Your best bet is to search amazon to see if there are any "laptop skins" specifically made for your model laptop. These are vinyl stickers which exactly fit the contours of your laptop, leaving all of the vents uncovered and functional. They come in a variety of imagery and textures.
Alternatively, you could create a jewelry cleaning kit as I described in this answer and use it on the remaining stains. You might get lucky and return your laptop to its original appearance.