All in one line:

my @data = map { [split] } <DATA>;
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Or, spelt out step by step...

my @data;
while ( <DATA> ) {      #for each line of data
    my @row = split;    #split on whitspace
    push @data, \@row;  #push a reference to the row
}

print "$data[0][0]\n";   #-2.65
print "$data[1][0]\n";   #-2.6

print "$data[1][1]\n";   #-2.0532e-006
print "$data[1][2]\n";   #2.0569e-006

__DATA__
-2.65 -2.0865e-006 2.0831e-006
-2.6 -2.0532e-006 2.0569e-006
-2.55 -2.0215e-006 2.0262e-006
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You didn't mention where the data originally comes from, so we can't help you with that.

See split, map and the Perl Data Structures Cookbook for more details.