If you empty your fish tank you'll lose all the beneficial bacteria.For that reason I wouldn't start over, unless your tank is in extremely bad condition. With a little elbow grease and a few simple cleaning supplies your aquarium can be ship shape again. Here's what you'll need:
Algae scraper/pad
Razor blade (plastic blade for acrylic tanks)
Bleach
Water siphon
Bucket
Lime remover/glass cleaner (made for aquariums)
Filter media
Filter brush
Old bath towels
Paper towels
I suggest cleaning your aquarium in the following order:
Inside glass
Decorations (rocks, plants, etc)
Gravel
Outside glass and fixtures
Filter
Algae Pads/Scrapers
Start by giving the glass a good cleaning on the inside with an algae pad. There are a wide variety of algae scrapers on the market, from long handled scrubbers to magnetic scrubbers. I personally like small magnetic scrubbers, but virtually any algae pad will do. Is it necessary to purchase algae pads at a pet shop instead of the the housewares department of a regular store? Although they may look the same, the housewares pads can have soap or chemical residue. That reside doesn't matter if you are cleaning your kitchen sink, but it can be lethal to your fish.
For stubborn residue on the glass, use a razor blade to scrape it off. Take care not to cut yourself. If your aquarium is acrylic, use a plastic razor blade, as standard razors will scratch acrylic.
Bleach
Once the inside glass is clean, remove rocks, artificial plants, or decorations that have significant algae growth, or are noticeably dirty. Do not clean them with soap or detergents. It's very difficult to completely remove soap, and even a trace can be lethal to fish. Usually a good scrub with an algae scraper will remove the algae and dirt from rocks and plants. For particularly stubborn cleaning problems, prepare a 10% bleach solution and soak the items for 15 minutes. Scrub any remaining residue off, rinse well in running water, and let air dry to eliminate residual bleach.
Live plants can bleached, however stem plants are not tolerant of bleaching. To bleach live plants prepare a 5% bleach solution, soak the plants for two to three minutes, then rinse well. Leave the rocks, decorations and plants out of the tank while you vacuum the gravel. That way none of the debris stirred up from the gravel will settle on them.
Tip - be sure to get a new bucket and designate it for aquarium use only. If you use a bucket that has had soap or detergent in it, you could introduce lethal chemicals to your tank.
Siphon
Clean the gravel next, by using a water siphon to vacuum away the debris. There are several types of siphons available, all of which work essentially the same. My preference is the Python, because it draws dirty water directly into your sink, thus eliminating the need for buckets. Magnum makes an adapter for the Hot Pro unit that allows you to siphon water through the filter and return the water back to the tank. Although this removes larger debris, smaller particles will pass through the filter and are returned to the tank. Be sure to vacuum the entire surface of the gravel thoroughly so that all debris is removed.
Glass and Lime Cleaners
Once the inside of the aquarium is cleaned, clean the hood, light, tank top, and outside glass. Regular glass cleaners contain ammonia, which is toxic to fish. Standard lime cleaners are even more toxic. I strongly urge using vinegar or cleaners designated as aquarium safe, and rinse rinse rinse!
Filter Cleaning
Once the outside is clean, the rocks, plants, and other decorations may be returned to the tank. Now wait a couple of weeks before cleaning the filter. Why wait? The major cleaning you just performed disturbed the beneficial bacterial colonies on the plants, rocks, and gravel. Fortunately many beneficial bacteria reside within the filter media, so you haven't completely upset the Eco-system. However if you changed the filter at the same time, you might trigger a dangerous ammonia spike because there aren't enough beneficial bacteria left to eliminate the toxins.
When you are ready to clean the filter, should you clean or simply replace the filter media entirely? Some experts caution that replacing the filter media removes too many of the beneficial bacteria, and triggers a new tank break-in cycle. Other experts argue that sufficient bacteria reside on the rocks,plants, and in the gravel to prevent the tank from cycling when the filter is replaced. I believe what you should do depends on the type of filter media you use.
If you have filter media containing carbon, ammonia absorbers, or ion-exchange resins, it should be replaced if it's more than three weeks old. After a couple of weeks the absorbing qualities of the media have been exhausted, and it no longer serves it's purpose. Media that acts as a mechanical filter instead of absorbing toxins (i.e.: ceramic rings, filter fiber, or sponges) should be gently rinsed to remove debris and returned to the filter instead of replaced. If care is taken to use water that is the same temperature as the aquarium water, and the media is quickly returned to the filter, the bacterial colonies growing on them will not be lost entirely.
Don't forget to clean the filter tubing and other parts of the filter assembly. A filter brush will help clear out the sludge that invariably builds up in all the small crevices.
Ongoing Maintenance
Once you've gotten your tank in shape, make sure you clean it on an ongoing basis so it never needs a major spring-cleaning again. Scrape the glass weekly, vacuum the gravel every time you perform a water change, and clean any rocks or plants as soon as you see debris or algae on them. Clean the filter monthly, either by replacing the media, or rinsing it. While you are at it, soak your fish nets in a disinfectant solution to keep them clean and soft. With regular care, your aquarium will look beautiful all the time.