If you have the names of the relevant transcripts in a text file, with one name per line, you can get them using the BBMap package like this:

filterbyname.sh in=trinity.fasta out=filtered.fasta names=names.txt include

You can also take a look to the faSomeRecords program. Think as an alternative to the previous one. The nice thing about this is that is written in C and is accompanied by a bunch of other useful programs It requires a 64bit environment, though