another take - using much of the same constructs as the OP, but also being aware of Tachyon's advice on .* - generally if you use a *, think twice. e.g. you originally used \d*\.\d*. - but if you tink about it, you probably done want to match '..' which \d* match (zero or more matches) 
#!/usr/bin/perl -w

use strict;

my @buf = <DATA>;
chomp @buf; # chop of all the line endings

my $doc = join ' ', @buf; # one nice juicy line
my $doc_id = qr(\d+\.\d+\.); # precomp regex - also self documenting

while ($doc =~ /($doc_id)\s+(\w+)(.*?)Prototype:.*?(?=$doc_id)?/g) {
    print "$1 $2 $3\n";
}

__DATA__
5.1. GetAFunctionHere
This is the description of a function
Which spans a few lines
Prototype:
int
GetAFunctionHere(int *count)

Parameters:
*count probably some kind of spelling object

5.2. GetMoreFunctionsHere
This is the description of another function
Which spans a few more lines
Prototype:
int
GetMoreFunctionHere(float *crash)

Parameters:
*crash probably some kind of rowing object

[download]
the (?=...) is a fancy way of saying 'look ahead till you find another doc_id string, but also start the next match from that doc_id' - it is called a zero-width positive look ahead assertion - zero width means it does not go into the $& match string (I think)(strings are normally consumed by $& as they match), positive means find this pattern in the source string (as opposed to 'find not this pattern in the string'), look ahead means peek forward, but do not move the regex internal position counter (accessible via pos()) and assertion, well that just seems redundant - like you'd go to all that trouble then say 'but that's just a suggestion'. I put the trailing ? after the (?=...) to catch the last doc string

In reply to Re: regex help by leriksen
in thread regex help by jai

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