Preheat oven to 350 degrees. Line a baking sheet with parchment. Trim tip end from a lemon so fruit sits level. Cut stem end one-third of the way down, making cut parallel with bottom; reserve top. Repeat with remaining lemons.
Hold a lemon above a sieve set over a bowl, and scoop out the pulp. Squeeze the juice from the pulp, and reserve. Repeat with all lemons. Place shells on prepared baking sheet.
Combine egg yolks, 1/4 cup granulated sugar, 1/4 cup reserved lemon juice, and flour in the heat-proof bowl of an electric mixer fitted with the whisk attachment. Beat mixture on medium speed until pale yellow, about 3 minutes. Place bowl over a pan of simmering water; whisk constantly until very thick, about 8 minutes. Remove bowl from heat, and return to mixer. Beat on medium speed until cool, scraping down sides several times, about 10 minutes. Transfer to a medium bowl, and set aside.
Combine egg whites and remaining 1/4 cup granulated sugar in clean mixer bowl. Place the bowl over the pan of simmering water, and stir until sugar has dissolved and mixture is warm to the touch. Remove bowl from heat, and return to mixer; beat on low speed until frothy. Gradually increase speed until meringue is shiny and holds soft peaks, 2 to 3 minutes, being careful not to overbeat.
Whisk 1/3 of the meringue into the yolk mixture. Gently fold in the remaining meringue. Carefully fill the prepared lemon shells to just below the rims.
Transfer baking sheet to oven, and bake until meringue is slightly golden and rises about 1 inch above the shell, about 14 minutes. Remove from oven, and transfer to serving plates. Garnish with the reserved lemon tops, and dust with confectioners' sugar. Serve immediately.