In the case of flowers as your 3D effect, the possibilities are as endless as the number of flowers!
For roses, your nail artist can create a set of nails that starts with a closed bud and with each successive nail on one hand that bud opens until your last nail (either your thumb or your pinky) is a full blooming rose.
The other option here is to make every nail a full blooming rose or make them all rosebuds for stunning 3D flower nails.
Other flowers that work well with this effect are peonies, carnations, and other multi-petal flowers.
With each of these, the nail artist has to painstakingly place petals and use a fast-drying nail lacquer to get the petals to stick and to stay.
Little details, such as leaves or petal veins, are added at the end to give your nail flowers rich looking realism.
One final option is flowers that are actually clusters of smaller flowers. For example, honeysuckle, lilacs and hyacinths are all flowers that are comprised of multiple smaller flowers.
When a nail artist does these in a 3D format, he/she uses nail polish pens to build up layers of a flower design until you have some raised projections and shadows that make these flowers look very three-dimensional on your nails.
Nail gems can also be used to create the tiny petals of these clusters of flowers and obtain the 3D effect you most desire.