The ISO standard ISO 2033:1983, and the corresponding Japanese Industrial Standard JIS X 9010:1984 (originally JIS C 6229–1984), define character encodings for OCR-A, OCR-B and E-13B. There are two major MICR fonts in use: E-13B and CMC-7. There is no particular international agreement on which countries use which font. In practice, this does not create particular problems as cheques and other vouchers do not usually flow out of a particular jurisdiction. The E-13B font has been adopted as an international standard in ISO 1004-1:2013, and is the standard in Australia, Canada, the United Kingdom, the United States, as well as Central America and much of Asia, besides other countries. The CMC-7 font has been adopted as an international standard in ISO 1004-2:2013, and is widely used in Europe, including France and Italy, Mexico, and South America, including Argentina, Brazil, Chile, besides other countries. Israel is the only country that can use both fonts simultaneously, though the practice makes the system significantly less efficient. This situation is the product of the Israelis adopting CMC-7, while the Palestinians opted for E-13B.

MICR characters are printed on documents in one of the two MICR fonts, using magnetizable (commonly known as magnetic) ink or toner, usually containing iron oxide. In scanning, the document is passed through a MICR reader, which performs two functions: magnetization of the ink, and detection of the characters. The characters are read by a MICR reader head, a device similar to the playback head of a tape recorder. As each character passes over the head, it produces a unique waveform that can be easily identified by the system. MICR readers are the primary tool for cheque sorting and are used across the cheque distribution network at multiple stages. For example, a merchant will use a MICR reader to sort cheques by bank and send the sorted cheques to a clearing house for redistribution to those banks. Upon receipt, the banks perform another MICR sort to determine which customer's account is charged and to which branch the cheque should be sent on its way back to the customer. However, many banks no longer offer this last step of returning the cheque to the customer. Instead, cheques are scanned and stored digitally. Sorting of cheques is done as per the geographical coverage of banks in a nation.

Before the mid-1940s, cheques were processed manually using the Sort-A-Matic or Top Tab Key method. The processing and cheque clearing was very time-consuming and was a significant cost in cheque clearance and bank operations. As the number of cheques increased, ways were sought for automating the process. Standards were developed to ensure uniformity in financial institutions. By the mid-1950s, the Stanford Research Institute and General Electric Computer Laboratory had developed the first automated system to process cheques using MICR. The same team also developed the E-13B MICR font. “E” refers to the font being the fifth considered, and "B" to the fact that it was the second version. The “13” refers to the 0.013-inch character grid. The trial of MICR E-13B font was shown to the American Bankers Association (ABA) in July 1956, which adopted it in 1958 as the MICR standard for negotiable documents in the United States. ABA adopted MICR as its standard because machines could read MICR accurately, and MICR could be printed using existing technology. In addition, MICR remained machine readable, even through overstamping, marking, mutilation and more. The first cheques using MICR were printed by the end of 1959. Although compliance with MICR standards was voluntary in the United States, it had been almost universally adopted in the United States by 1963. In 1963, ANSI adopted the ABA's E-13B font as the American standard for MICR printing, and E-13B was also standardized as ISO 1004:1995.

One of the biggest problems found in the second phase was how to input the check information, especially the account numbers, with any sort of speed. Beise demanded a system that would not require the information to be changed from one medium to another, from check to punched card for instance, while simultaneously lowering error rates. SRI investigated several solutions to the problem, including the first OCR system from a company in Arlington, Virginia. However, they found that it was all too easy for banks, and customers, to write over the account numbers and spoil the system. They also experimented with barcode information, and while this worked well even when printed over, if there was enough "damage" to the code a human operator could not read them in order to input them manually. Instead, they decided to combine the two technologies, and used MICR-printed account numbers which could be read by a magnetic reader similar to those in a cassette tape recorder. The resulting reader was a mechanical tour-de-force, combining five MICR readers with a large rotating drum that forced checks dumped in the top to come out the bottom single-file. The system was eventually able to read ten checks a second, with errors on the order of 1 per 100,000 checks.