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This system works well if you are still building your collection and most of your cards are collected into decks. Simply place your cards into an empty deck box and place the box somewhere convenient, like on a shelf or in your closet. Since you've likely started to change your decks to be stronger when playing, you may want to name or label your decks so you know exactly what each box contains. For example, you might put a piece of tape on a box and write on the tape, "Psychic Pokemon Deck." There are many card collecting games similar to the Pokemon TCG (trading card game). These have frequently made use of binders, and this method of organization might be right for you. This format will allow a clear view of your cards and easy access. It will also protect your cards from damage, like bending and mold. These trading card binders are often filled with plastic inserts which have pockets for your cards. You can buy inserts like this from your local board game/hobby store. You might also make use of tabs to help you easily navigate your binder. Binder tabs can be bought at most office supply stores. You can make your own simple tab by fastening a piece of tape to the front and back of your plastic insert, allowing some extra tape to stick out from your binder. Then write the heading on your tab, for example, you might write, "Type: Grass." This method is best for serious collectors who have thousands of cards to keep track of. A card catalog is usually a large, wooden piece of furniture filled with narrow drawers into which you can put cards. You can find card catalogs at flea markets, garage sales, eBay, CraigsList, and antique stores, though antique catalogs may be expensive. If you purchase your card catalog secondhand, you should inspect it carefully. Many of these are old, and you might have to spend some time or money restoring it to hold your cards safely and securely. You can buy narrow box-sleeves that are designed to hold your cards at your local game/hobby store, office supply store, or online. There are also larger boxes intended specifically for storing trading cards that you could easily use for your Pokemon cards. After you organize your cards you can store your collection in these boxes, you can label each box according to your system of organization. For example, you might label one box, "Fighting Type," and another "High HP Pokemon."
Organize by deck boxes. Use a binder. File cards away into a card catalog. Separate cards into storage boxes.