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Just copy each layer over from Illustrator to a new InDesign Layer.
Check your copy settings in Illustrator preferences before you do this.
From Adobe Help-
The Clipboard
You can use the Clipboard to transfer selections between an Illustrator file and other Adobe applications including Adobe Photoshop, Adobe GoLive, and Adobe InDesign. The Clipboard is particularly useful for importing paths because paths are copied to the Clipboard as PostScript language descriptions. Artwork copied to the Clipboard is pasted in PICT format in most applications. However, some applications take the PDF version (such as InDesign) or the AICB version. PDF preserves transparency; AICB lets you specify whether you want to preserve the overall appearance of the selection or copy the selection as a set of paths (which can be useful in Photoshop).
To specify copying preferences, choose Edit > Preferences > File Handling & Clipboard (Windows) or Illustrator > Preferences > File Handling & Clipboard (Mac OS). Select PDF, AICB, or both. If you select AICB, select Preserve Paths to discard any transparency in the copied artwork or Preserve Appearance and Overprints to flatten any transparency, maintain the copied artwork’s appearance, and preserve overprinted objects.
OR Copy as layered PDF and when Placing into InDesign-
To set layer visibility
You can set the visibility of layers in Photoshop PSD files or layered PDF files as you place them. If the Photoshop PSD file contains layer comps, you can choose which comp you want to display.
Do one of the following:
To import a graphic without first creating a frame, make sure that nothing in the document is selected.
To import a graphic into an existing frame, select the frame.
To replace an existing image, select the graphics frame.
Choose File > Place and select a graphics file.
To view Version Cue options, click Use Adobe Dialog.
If you want to replace a selected object, select Replace Selected Item.
Select Show Import Options, and then click Open.
In the Image Import Options or Place PDF dialog box, click the Layers tab.
To view a preview of the image, click Show Preview.
(PDF files only) If you are placing a page from multipage PDF file, click the arrows, or type a page number under the preview image to preview a specific page.
(Photoshop PSD files only) If the image contains layer comps, choose the layer comp you want to display from the Layer Comp pop-up menu.
Do one of the following:
To open or close a layer set, click the triangle to the left of the folder icon.
To hide a layer or layer set, click the eye icon next to the layer or layer set.
To display the layer or layer set, click the empty eye column next to the layer or layer set.
To display only the content of a particular layer or layer set, Alt-click (Windows) or Option-click (Mac OS) its eye icon. Alt-click (Windows) or Option-click (Mac OS) the eye icon again to restore the original visibility settings of the other layers.
To change the visibility of multiple items, drag through the eye column.
Set the When Updating Link option as desired:
Use Photoshop’s/PDF’s Layer Visibility Matches the layer visibility settings to those of the linked file when you update the link.
Keep Layer Visibility Overrides Maintains the layer visibility settings as specified in the InDesign Document.
Click OK.
Do one of the following:
To import into a new frame, click the loaded graphics icon in the layout at the place where you want the upper left corner of the graphic to appear.
To import into an existing, unselected frame, click the loaded graphics icon anywhere in that frame.
To import into an existing selected frame, you don’t need to do anything; the image automatically appears in that frame.
If you accidently replace an existing graphic with an image you’re placing, press Ctrl+Z (Windows) or Command+Z (Mac OS) to return the original image to the frame and display the loaded graphics icon.
Of course you could also just save each layer as a separate Illustrator .ai or .eps file and place those on layers in Indesign, but thats old school.
Adobe's Application built in Help is pretty good, check it out next time your in a bind.
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