should those sub-directories be named the same way you would use the ccTLD?
According to the Google Webmaster Tools on Multi-regional and multilingual sites under "URL structures" for subdirectories, you can use gTLDs as a subdirectory, however, as Google states here in regards specifying which URLs to use for multilingual regions:
Do not specify a country code by itself! Google does not automatically derive the language from the country code.
So for a country like South Africa which has multiple languages, you should use codes that specify the language in the ISO 639-1 format with the region using the ISO 3166-1 Alpha 2 format. The first example given there is for Ireland:
en for English and
ie for Ireland).
For example the ccTLD for South Africa is .za so should my sub-directory be www.mysite.com/za/?
As indicated above, the format for an English version for South Africa would be:
If you want to provide other versions (e.g.,
af for Afrikaans), then just follow the guidelines from Google on how to use hreflang for language and regional URLs to indicate to Google which language and regional version to serve in their search results.
Also, is there a ccTLD for Africa and South America as a whole or is it best to target each individual country?
There isn't a ccTLD for these continents as a whole since they're made up of many countries, some of which speak several different languages (e.g., South Africa). Therefore it's best to target them individually by language and region as covered above.