Create Feed Wrangler "smart streams" matching your Google Reader folders. First import your feeds from Google Reader, export your Reader OPML file to the script directory, edit the script to include your user name and password, then run it. Note Feed Wrangler has since added this feature, so this script should no longer be necessary!

feedfolder.rb

#!//usr/bin/env ruby
require 'bundler/setup'
require 'opml_saw'
require 'json'
require 'net/https'
require 'uri'

#
# Enter your email and password for feedwrangler below
#
user_email = "YOUR EMAIL HERE"
password = "YOUR PASSWORD HERE"

# Gemfile:
# source 'https://rubygems.org'
# gem 'nokogiri'
# gem 'opml_saw', :git => "git://github.com/feedbin/opml_saw.git", :branch => "master"

#
# subscriptions.xml is the OPML file from Google Reader Takeout
# Extract it and put it in the same directory you run this script from.
#
file = File.open('subscriptions.xml', 'r')
contents = file.read
opml = OpmlSaw::Parser.new(contents)
opml.parse

folders = {}
opml.feeds.each do |feed| 
  if feed.has_key? :tag 
    unless folders.has_key? feed[:tag] 
      folders[feed[:tag]] = []
    end
    folders[feed[:tag]].push feed[:xml_url]
  end
end

site = Net::HTTP.new("feedwrangler.net", 443)
site.use_ssl = true
uri = "/api/v2/users/authorize?email=#{user_email}&password=#{URI.escape(password)}&client_key=7d321aef757b8f6e83e39041e37738ec"
response = site.get2(uri)
token = ""
if response.code == "200" 
  fwfeeds = JSON.parse(response.body)
  token = fwfeeds["access_token"]
else
  puts "Unable to retrieve subscription list from feedwrangler.net: #{response.code} #{response.message}"
  response.each { |key, val| printf "%-14s = %-40.40s\n", key, val }
  p response.body[400, 55]
  exit 
end
feedindex = {}
fwfeeds["feeds"].each do |feed| 
  feedindex[feed["feed_url"]] = feed["feed_id"]
end

folders.each do |name, feedurls|
  feedids = []
  feedurls.each do |feedurl|
    if feedindex.has_key? feedurl 
      feedids.push feedindex[feedurl]
    end
  end
  folders[name] = feedids
end

folders.each do |name, feedids|
  uri = "/api/v2/streams/create?access_token=#{token}&title=#{URI.escape(name)}&only_unread=true&all_feeds=false&feed_ids=#{feedids.join(',')}"
  response = site.get2(uri)
  puts "Create \"#{name}\": #{response.code} #{response.message}"
end