Before you start to prune you have to know whether your tomato plants are determinate or indeterminate plants. Determinate tomato plants are compact or somewhat bushy with short branches and clusters of flowers at the end. This type of tomato plants are in full growth before bearing fruit and do not require pruning. In fact pruning them will probably destroy the plant. If your plants are more upright as opposed to bushy then you have indeterminate tomato plants that should be pruned to get the best growth and flavor.
Shoots that should be removed are the growths that have no buds or flowers. Essentially they are nothing more than suckers that take nutrients from the plant. Pruning maximizes the natural process of plant photosynthesis where the sun is the energy source to produce carbohydrates. In an ideal situation every leaf is exposed to the sun. Each leaf stem exposed to the sun fills with sugar including stems and leaves that produce no fruit. These are the shoots and leaves that need to be removed to increase optimum fruit. Essentially they are robbing sugar from the fruit producing shoots.
Start pruning from the bottom
Once the tomato plants are about 3 feet or 1m tall, remove all the leaves from the bottom 30cm or first foot of the stem. These tomato leaves will be the first leaves to develop fungus because they get the least amount of sun and soil pathogens can be unintentionally splashed up onto them.
A well-pruned young plant
Pruning also minimizes the risk of disease. It actually helps improve plant health by exposing more leaves and shoots to the sun. Pruned plants allow dry leaves to fall off faster reducing bacterial and fungal. To aid in this process the plants should be staked or grown in baskets to prevent them from falling upon the ground and becoming shaded from the sun. If a plant or a portion of the plant is shaded from the sun it will not mature and produce little to no fruit.
Once the plant has 2-3 good trusses of tomatoes, start from the base of the plant and pinch off the unnecessary shoots and leaves leaving only the fruit producing shoots. Later on in the season as the plant reaches full growth the top leaves and shoots should be removed to allow the plant to continue to receive sun energy to produce fruit.