Mineral deposits can occur when there is a high concentration of minerals such as magnesium, potassium and calcium in your water. This is known as hard water and can become a problem for your drains and pipes if not prevented or removed. These minerals are picked up by groundwater as it flows through the soil and rocks.
You will notice if you have hard water build up when there are whites stains on the surfaces of your appliances and household items such as your toilets, sinks, dishwasher and even your dishes. If left untreated or not removed, hard water build up can cause some serious issues to your plumbing, but also your health.
Calcium buildup, also known as limescale, can be dissolved by using acids but it is a rarity for buildups to occur in copper pipes. Although it is possible, the levels of Calcium will need to be extremely high. If you see hard water build up occurring, you'll need to install a water softener to treat the water. This will not only save your pipes, but also your washing machine, dishwasher and toilets.
Solutions like CLR drain cleaner can reduce the amount of hard water build up in your drains and pipes, but this is not a longer term solution. CLR Drain cleaners are also toxic and damaging when it comes in contact with skin so this is not a fully recommended solution. However, if you are just looking to clean the outside of your fixture like your shower head and faucets then CLR drain cleaner will work perfectly for that purpose.
As far as removing the calcium from the inside of the copper pipes, there is nothing you can put into the pipes that you would want to drink later. No governmental agency will allow plumbers to treat the inside of copper pipes because of the hazards involved. CLR drain cleaners won't permanently fix the issue either and these solutions also contain toxic chemicals you wouldn't want in your drinking water.
You could use vinegar in the pipes, but it would take a lot of vinegar and you would have to leave it in the pipes at least 24 hours. You would have to remove all of the water in the pipes and replace it with vinegar. Vinegar dissolves calcium and minerals. Then you would have to flush your pipes. The vinegar taste may be in the pipes for some time afterwards, but it is completely harmless versus store bought CLR drain cleaners.
A better solution is to simply replace the pipes with PEX plastic pipes. Plastic is completely resistant to any mineral build-up and provides higher pressures and water flow rates than copper pipe. A Roto-Rooter plumber can evaluate your pipes and give you some options.