In a nutshell you seem to assume .* will match newlines. It won't without a /s When you add a /s to .* it will match everything, so you generally need .*? to make it less greedy but this involves backtracking and is inefficient. See Death To Dot Star!. Note dot star does have its uses, but there are often better ways to skin your cat. You also use m/\d*\.\d*\./ which will match '..' which is not what you want. It should be \d+ in the context shown.

Essentially all you are doing is grabbing two lines at a time (by the looks). Here are some example approaches. The best one depends on the exact format and consitency of the data. Where possible using the input record separator to chunkify an input stream into records is often the easiest approach. You can often then just split the record to get the bits you want. Anyway:

# example 1
my $flag = 0;
while(<DATA>) {
    next unless $flag or m/^\d+\.\d+/;
    print;
    $flag ^= 1;
}

# example 2 depends on newline before Prototype section
# using input record separtator to do the work
$/ = "\n\n";
while(<DATA>) {
    print if m/^\d+\.\d+\./;
}

# example 3 one of many possible REs
local $/;
$data = <DATA>;
@chunks = $data =~ m/^(\d+\.\d+\.[^\n]+\n[^\n]+\n)/gm;
print @chunks;

# example 4 yet another way to do it (LIKE YOUR ORIGINAL)
local $/;
$data = <DATA>;
@chunks = $data =~ m/(^\d+\.\d+\..*?(?=Prototype:))/gsm;
print @chunks;

__DATA__
5.1. GetTagBytestoWrite
This function returns the number of bytes taken by the Tag of the ASN 
+object. It Scans through the BER/DER encoded String and finds the no 
+of bytes taken by the Tag of a given ASN.1 Object.

Prototype:
 int
GetTagbytestoWrite(unsigned char *tstr,int *count)
Parameters:
*tstr Contents of the ASN.1 Object in a string
*count a pointer to an integer to hold the address of the variable hol
+ding the number of bytes the tag value takes to store itself.

5.2. GetLenBytestoWrite
This function returns the no of Octets taken by the Length field of a 
+given ASN.1 Object. It Scans through the BER/DER encoded String and f
+inds the no of bytes taken by the Length field of a given ASN.1 Objec
+t.

Prototype:
 int
GetLenbytestoWrite(unsigned char *pstr,int *count)
Parameters:
*pstr Contents
..
[download]

cheers

tachyon

s&&rsenoyhcatreve&&&s&n.+t&"$'$`$\"$\&"&ee&&y&srve&&d&&print

#!/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]

perl -n00e 'print if /^\d/;' filename

However, since the second prototype doesn't have a blank line, you need to take that into account, with something like:

perl -n00e '/^(\d(.(?!\nPrototype))+)/ms; print $1' filename

This will search for any paragraph that starts with a number, then look for as many characters as it can find that aren't followed by \nPrototype.

If the file doesn't have a blank line before each function definition (except the first), then this won't work, though.

I noticed your code references an HTML file. Are we looking at the raw file here, or the cut-n-paste from a browser? If the raw file is laid out with HTML tags, that will complicate things, and these solutions may not work.