You may send handwritten 1099s to the IRS provided that you are sending fewer than 250 of them. Anyone required to file more than 250 versions of a single form must file them electronically. The IRS publication 1220, updated yearly, explains the electronic filing process for form 1099 and forms like it.
Make sure that your handwriting is legible and unambiguous, and double-check every number you enter, especially ID numbers like your Social Security or Taxpayer Identification Numbers. Letters should be block-printed and clear, particularly on Copy A of the 1099, which will be read by machine.
Dollar signs are pre-preprinted on the form; do not add dollar signs of your own. Ampersands, asterisks, commas and apostrophes should all be eschewed as well, as should number signs -- "APT 4" rather than "APT #4." Do include the decimal points and cents of each value you write in a number box, and if a box requires no entry, leave it blank rather than entering zeroes.
In the section of the 1099 rules allowing handwritten forms, the IRS recommends working with an IRS-partnered tax aid to ensure that everything on your form is accurate and doesn't conflict. You can find such IRS partners by going to IRS.gov and typing "e-file for business partners" into the Search box.